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Sample records for arm docking complex

  1. Docking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro.

    Science.gov (United States)

    Oda, Toshiyuki; Abe, Tatsuki; Yanagisawa, Haruaki; Kikkawa, Masahide

    2016-04-15

    The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs can bind to DMTs and porcine microtubules with 24-nm periodicities even in the absence of the docking complexin vitro Using cryo-electron tomography and structural labeling, we observed that the docking complex took an unexpectedly flexible conformation and did not lie along the length of DMTs. In the absence of docking complex, ODAs were released from the DMT at relatively low ionic strength conditions, suggesting that the docking complex strengthens the electrostatic interactions between the ODA and DMT. Based on these results, we conclude that the docking complex serves as a flexible stabilizer of the ODA rather than as a molecular ruler. PMID:26933181

  2. Characterization of a subunit of the outer dynein arm docking complex necessary for correct flagellar assembly in Leishmania donovani.

    Directory of Open Access Journals (Sweden)

    Simone Harder

    Full Text Available BACKGROUND: In order to proceed through their life cycle, Leishmania parasites switch between sandflies and mammals. The flagellated promastigote cells transmitted by the insect vector are phagocytized by macrophages within the mammalian host and convert into the amastigote stage, which possesses a rudimentary flagellum only. During an earlier proteomic study of the stage differentiation of the parasite we identified a component of the outer dynein arm docking complex, a structure of the flagellar axoneme. The 70 kDa subunit of the outer dynein arm docking complex consists of three subunits altogether and is essential for the assembly of the outer dynein arm onto the doublet microtubule of the flagella. According to the nomenclature of the well-studied Chlamydomonas reinhardtii complex we named the Leishmania protein LdDC2. METHODOLOGY/PRINCIPAL FINDINGS: This study features a characterization of the protein over the life cycle of the parasite. It is synthesized exclusively in the promastigote stage and localizes to the flagellum. Gene replacement mutants of lddc2 show reduced growth rates and diminished flagellar length. Additionally, the normally spindle-shaped promastigote parasites reveal a more spherical cell shape giving them an amastigote-like appearance. The mutants lose their motility and wiggle in place. Ultrastructural analyses reveal that the outer dynein arm is missing. Furthermore, expression of the amastigote-specific A2 gene family was detected in the deletion mutants in the absence of a stage conversion stimulus. In vitro infectivity is slightly increased in the mutant cell line compared to wild-type Leishmania donovani parasites. CONCLUSIONS/SIGNIFICANCE: Our results indicate that the correct assembly of the flagellum has a great influence on the investigated characteristics of Leishmania parasites. The lack of a single flagellar protein causes an aberrant morphology, impaired growth and altered infectiousness of the parasite.

  3. CCDC151 mutations cause primary ciliary dyskinesia by disruption of the outer dynein arm docking complex formation

    DEFF Research Database (Denmark)

    Hjeij, Rim; Onoufriadis, Alexandros; Watson, Christopher M;

    2014-01-01

    disorder of ciliary and flagellar dysmotility characterized by chronic upper and lower respiratory infections and defects in laterality. Here, by combined high-throughput mapping and sequencing, we identified CCDC151 loss-of-function mutations in five affected individuals from three independent families...... whose cilia showed a complete loss of ODAs and severely impaired ciliary beating. Consistent with the laterality defects observed in these individuals, we found Ccdc151 expressed in vertebrate left-right organizers. Homozygous zebrafish ccdc151(ts272a) and mouse Ccdc151(Snbl) mutants display a spectrum...... of situs defects associated with complex heart defects. We demonstrate that CCDC151 encodes an axonemal coiled coil protein, mutations in which abolish assembly of CCDC151 into respiratory cilia and cause a failure in axonemal assembly of the ODA component DNAH5 and the ODA-DC-associated components...

  4. Four-arm single docking full robotic surgery for low rectal cancer: technique standardization

    Directory of Open Access Journals (Sweden)

    José Reinan Ramos

    2014-06-01

    Full Text Available The authors present the four-arm single docking full robotic surgery to treat low rectal cancer. The eight main operative steps are: 1- patient positioning; 2- trocars set-up and robot docking; 3- sigmoid colon, left colon and splenic flexure mobilization (lateral-to-medial approach; 4-Inferior mesenteric artery and vein ligation (medial-to-lateral approach; 5- total mesorectum excision and preservation of hypogastric and pelvic autonomic nerves (sacral dissection, lateral dissection, pelvic dissection; 6- division of the rectum using an endo roticulator stapler for the laparoscopic performance of a double-stapled coloanal anastomosis (type I tumor; 7- intersphincteric resection, extraction of the specimen through the anus and lateral-to-end hand sewn coloanal anastomosis (type II tumor; 8- cylindric abdominoperineal resection, with transabdominal section of the levator muscles (type IV tumor. The techniques employed were safe and have presented low rates of complication and no mortality.

  5. Synaptotagmin-1 docks secretory vesicles to syntaxin-1/SNAP-25 acceptor complexes

    DEFF Research Database (Denmark)

    de Wit, Heidi; Walter, Alexander M; Milosevic, Ira; Gulyás-Kovács, Attila; Riedel, Dietmar; Sørensen, Jakob B; Verhage, Matthijs

    2009-01-01

    the minimal docking machinery. Moreover, we show that the requirement for Munc18-1 in docking, but not fusion, can be overcome by stabilizing syntaxin/SNAP-25 acceptor complexes. These findings, together with cross-rescue, double-knockout, and electrophysiological data, lead us to propose that......Docking, the initial association of secretory vesicles with the plasma membrane, precedes formation of the SNARE complex, which drives membrane fusion. For many years, the molecular identity of the docked state, and especially the vesicular docking protein, has been unknown, as has the link to...... SNARE complex assembly. Here, using adrenal chromaffin cells, we identify the vesicular docking partner as synaptotagmin-1, the calcium sensor for exocytosis, and SNAP-25 as an essential plasma membrane docking factor, which, together with the previously known docking factors Munc18-1 and syntaxin, form...

  6. Standardized single docking, four arms and fully robotic proctectomy for rectal cancer: the key points are the ports and arms placement.

    Science.gov (United States)

    Bertrand, Martin Marie; Colombo, Pierre-Emmanuel; Mourregot, Anne; Traore, Drissa; Carrère, Sébastien; Quénet, François; Rouanet, Philippe

    2016-06-01

    Rectal cancer continues to be a surgical challenge. As more technology is developed, the surgeon must both incorporate this new technology into his practice and, at the same time, keep improving oncologic surgery and overall outcomes. We describe a standardized approach and fully robotic proctectomy, using four arms and one single docking (SI system). Patient cart and ports placement, as well as arms position to avoid collision, are key points to perform the entire procedure with one single docking. Although the place of robotic surgery might still need to be defined, standardizing the procedures is a step towards its evaluation. We propose with this report a solution to perform a single docking four arms robotic proctectomy. PMID:26645073

  7. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    Science.gov (United States)

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures. PMID:26846813

  8. Accounting for complex entities: implications for ARMS

    OpenAIRE

    Moss, Charles B.; Klinefelter, Danny A.

    2012-01-01

    Purpose – The purpose of this research is to examine the effect of accounting for complex organizational forms on data collection with the Agricultural Resource Management Survey (ARMS). Design/methodology/approach – This research reviews the literature from accounting theory along with the goals of data collection for policy analysis to draw conclusions about the applicability of accounting pronouncements. Findings – Historically, the financial data collected in ARMS were based on financial ...

  9. Theoretical Studies on Docking Dynamics and Electronic Structure in Metalloprotein Complexes

    Science.gov (United States)

    Sugiyama, Ayumu; Nishikawa, Keigo; Yamamoto, Tetsunori; Purqon, Acep; Nishikawa, Kiyoshi; Nagao, Hidemi

    2007-12-01

    An investigating of docking structure and dynamics between metalloprotein is interested from the viewpoint of searching the function of protein. We investigate the cytochrome c551 and azurin complexes by three computational methods, quantum mechanical calculation, docking searching algorism and molecular dynamics simulation. At first we present the docking structure of the cytochrome c551-azurin complexes expected by ZDOCK searching algorism. Quantum chemical calculation is tools to estimate the charge distrubution around the active site for each protein and force field parameters. From these parameters, we reproduce the protein docking dynamics by molecular dynamics simulation. We analyze some physical properties of complex system such as binding free energy, dynamical cross correlation map, and so on. We discuss the docking stability and dynamical effect of the cytochrome c551-azurin complexes.

  10. A holistic molecular docking approach for predicting protein-protein complex structure

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

  11. Docking stability and electronic structure of azurin-cytochrome c551 complex system

    Science.gov (United States)

    Sugiyama, Ayumu; Takamatsu, Yuichiro; Nishikawa, Keigo; Nagao, Hidemi; Nishikawa, Kiyoshi

    We investigate the docking structure between cytochrome c551 and azurin proteins by quantum mechanical calculation and molecular dynamics (MD). A model for the docking structure of the cytochrome-azurin complex is presented. We calculate the charge distribution around the active site for each protein and force field parameters to simulate the complex system by MD. We estimate some physical properties, such as binding free energy and the dynamical cross-correlation map. We discuss the stability of the cytochrome c551-azurin complex system.

  12. FlexAID: Revisiting Docking on Non-Native-Complex Structures.

    Science.gov (United States)

    Gaudreault, Francis; Najmanovich, Rafael J

    2015-07-27

    Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specific geometric criteria, based on surface complementarity. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. The prediction of binding poses is tested using the widely used Astex dataset as well as the HAP2 dataset, while performance in virtual screening is evaluated using a subset of the DUD dataset. We compare FlexAID to AutoDock Vina, FlexX, and rDock in an extensive number of scenarios to understand the strengths and limitations of the different programs as well as to reported results for Glide, GOLD, and DOCK6 where applicable. The most relevant among these scenarios is that of docking on flexible non-native-complex structures where as is the case in reality, the target conformation in the bound form is not known a priori. We demonstrate that FlexAID, unlike other programs, is robust against increasing structural variability. FlexAID obtains equivalent sampling success as GOLD and performs better than AutoDock Vina or FlexX in all scenarios against non-native-complex structures. FlexAID is better than rDock when there is at least one critical side-chain movement required upon ligand binding. In virtual screening, FlexAID results are lower on average than those of AutoDock Vina and rDock. The higher accuracy in flexible targets where critical movements are required, intuitive PyMOL-integrated graphical user interface and free source code as well as precompiled executables for Windows, Linux, and Mac OS make FlexAID a welcome addition to the arsenal of existing small-molecule protein docking methods. PMID

  13. Structure prediction of protein complexes by an NMR-based protein docking algorithm

    International Nuclear Information System (INIS)

    Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the protein-protein docking problem, where the input consists of the tertiary structures of proteins A and B plus an unassigned one-dimensional 1H-NMR spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a 'theoretical' 1H-NMR spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental one. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. [Morelli et al. (2000) Biochemistry, 39, 2530-2537]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with four protein complexes whose three-dimensional structures are stored in the PDB data bank [Bernstein et al. (1977)] and whose 1H-NMR shift assignments are available from the BMRB database. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives

  14. On docking, scoring and assessing protein-DNA complexes in a rigid-body framework.

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    Marc Parisien

    Full Text Available We consider the identification of interacting protein-nucleic acid partners using the rigid body docking method FTdock, which is systematic and exhaustive in the exploration of docking conformations. The accuracy of rigid body docking methods is tested using known protein-DNA complexes for which the docked and undocked structures are both available. Additional tests with large decoy sets probe the efficacy of two published statistically derived scoring functions that contain a huge number of parameters. In contrast, we demonstrate that state-of-the-art machine learning techniques can enormously reduce the number of parameters required, thereby identifying the relevant docking features using a miniscule fraction of the number of parameters in the prior works. The present machine learning study considers a 300 dimensional vector (dependent on only 15 parameters, termed the Chemical Context Profile (CCP, where each dimension reflects a specific type of protein amino acid-nucleic acid base interaction. The CCP is designed to capture the chemical complementarities of the interface and is well suited for machine learning techniques. Our objective function is the Chemical Context Discrepancy (CCD, which is defined as the angle between the native system's CCP vector and the decoy's vector and which serves as a substitute for the more commonly used root mean squared deviation (RMSD. We demonstrate that the CCP provides a useful scoring function when certain dimensions are properly weighted. Finally, we explore how the amino acids on a protein's surface can help guide DNA binding, first through long-range interactions, followed by direct contacts, according to specific preferences for either the major or minor grooves of the DNA.

  15. Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking

    OpenAIRE

    Mouradov, Dmitri; Craven, Ari; Forwood, Jade Kenneth; Flanagan, Jack U.; García-Castellanos, Raquel; Gomis-Rüth, F. Xavier; Hume, David A.; Martin, Jennifer Lynn; Kobe, Bostjan; Huber, Thomas

    2006-01-01

    We have determined the three-dimensional structure of the protein complex between latexin and carboxypeptidase A using a combination of chemical cross-linking, mass spectrometry and molecular docking. The locations of three intermolecular cross-links were identified using mass spectrometry and these constraints were used in combination with a speed-optimised docking algorithm allowing us to evaluate more than 3 × 1011 possible conformations. While cross-links represent only limited structural...

  16. NMR-guided molecular docking of a protein-peptide complex based on ant colony optimization.

    Science.gov (United States)

    Korb, Oliver; Möller, Heiko M; Exner, Thomas E

    2010-07-01

    Standard docking approaches used for the prediction of protein-ligand complexes in the drug development process have problems identifying the correct binding mode of large flexible ligands. Herein we show how additional experimental data from NMR experiments can be used to predict the binding mode of a mucin 1 (MUC-1) pentapeptide recognized by the breast-cancer-selective monoclonal antibody SM3. Distance constraints derived from trNOE and saturation transfer difference NMR experiments are combined with the docking approach PLANTS. The resulting complex structures show excellent agreement with the NMR data and with a published X-ray crystal structure. The method was then further tested on two complexes in order to demonstrate its more general applicability: T-antigen disaccharide bound to Maclura pomifera agglutinin, and the inhibitor SBi279 bound to S100B protein. Our new approach has the advantages of being fully automatic, rapid, and unbiased; moreover, it is based on relatively easily obtainable experimental data and can greatly increase the reliability of the generated structures. PMID:20486157

  17. Asynchronous Complex Pipeline Design Based on ARM Instruction Set

    Institute of Scientific and Technical Information of China (English)

    WANG Bing; WANG Qin; PENG Rui-hua; FU Yu-zhuo

    2008-01-01

    This paper proposes an asynchronous complex pipeline based on ARM-V3 instruction set. Muller pipeline structure is used as prototype, and the factors which may affect pipeline performance are analyzed. To balance the difficulty of asynchronous design and performance analysis, both complete asynchronous and partial asynchronous structures aere designed and compared. Results of comparison with the well-Rnown industrial product ARM922T verify that about 30% and 40% performance improvement of the partial and complete asynchronous complex pipelines can be obtained respectively. The design methodologies can also be used in the design of other asynchronous pipelines.

  18. Assembly factors for the membrane arm of human complex I

    Science.gov (United States)

    Andrews, Byron; Carroll, Joe; Ding, Shujing; Fearnley, Ian M.; Walker, John E.

    2013-01-01

    Mitochondrial respiratory complex I is a product of both the nuclear and mitochondrial genomes. The integration of seven subunits encoded in mitochondrial DNA into the inner membrane, their association with 14 nuclear-encoded membrane subunits, the construction of the extrinsic arm from 23 additional nuclear-encoded proteins, iron–sulfur clusters, and flavin mononucleotide cofactor require the participation of assembly factors. Some are intrinsic to the complex, whereas others participate transiently. The suppression of the expression of the NDUFA11 subunit of complex I disrupted the assembly of the complex, and subcomplexes with masses of 550 and 815 kDa accumulated. Eight of the known extrinsic assembly factors plus a hydrophobic protein, C3orf1, were associated with the subcomplexes. The characteristics of C3orf1, of another assembly factor, TMEM126B, and of NDUFA11 suggest that they all participate in constructing the membrane arm of complex I. PMID:24191001

  19. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.

    Science.gov (United States)

    Wang, Zhe; Sun, Huiyong; Yao, Xiaojun; Li, Dan; Xu, Lei; Li, Youyong; Tian, Sheng; Hou, Tingjun

    2016-05-14

    As one of the most popular computational approaches in modern structure-based drug design, molecular docking can be used not only to identify the correct conformation of a ligand within the target binding pocket but also to estimate the strength of the interaction between a target and a ligand. Nowadays, as a variety of docking programs are available for the scientific community, a comprehensive understanding of the advantages and limitations of each docking program is fundamentally important to conduct more reasonable docking studies and docking-based virtual screening. In the present study, based on an extensive dataset of 2002 protein-ligand complexes from the PDBbind database (version 2014), the performance of ten docking programs, including five commercial programs (LigandFit, Glide, GOLD, MOE Dock, and Surflex-Dock) and five academic programs (AutoDock, AutoDock Vina, LeDock, rDock, and UCSF DOCK), was systematically evaluated by examining the accuracies of binding pose prediction (sampling power) and binding affinity estimation (scoring power). Our results showed that GOLD and LeDock had the best sampling power (GOLD: 59.8% accuracy for the top scored poses; LeDock: 80.8% accuracy for the best poses) and AutoDock Vina had the best scoring power (rp/rs of 0.564/0.580 and 0.569/0.584 for the top scored poses and best poses), suggesting that the commercial programs did not show the expected better performance than the academic ones. Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs. However, for some types of protein families, relatively high linear correlations between docking scores and experimental binding affinities could be achieved. To our knowledge, this study has been the most extensive evaluation of popular molecular docking programs in the last five years. It is expected that our work

  20. Novel water soluble neutral vanadium(IV)-antibiotic complex: Antioxidant, immunomodulatory and molecular docking studies.

    Science.gov (United States)

    Datta, Chitraniva; Das, Dharitri; Mondal, Paritosh; Chakraborty, Biswajit; Sengupta, Mahuya; Bhattacharjee, Chira R

    2015-06-01

    A novel water soluble five coordinate oxovanadium(IV) complex, [VO(C16H15N4O8S)HSO4] incorporating cefuroxime, a cephalosporin group of antibiotic have been prepared from an interaction of vanadyl sulfate and cefuroxime in aqueous solution. The compound was characterized by Fourier transform infrared spectroscopy (FTIR), CHN microanalyses, ultraviolet-visible spectroscopy (UV-Vis), fast atom bombardment (FAB) mass spectrometry and thermogravimetric analysis (TGA). Density Functional Theory (DFT) computation using Gaussian 09 program at B3LYP level revealed a distorted square pyramidal energy optimized geometry for the vanadyl(IV) complex. The molecular docking studies show that the interaction between the vanadium complex and protein receptor, clathrin is dominated by hydrophobic forces. The experimental (1)H nuclear magnetic resonance (NMR) features of the analogous Zn(II) complex matched well with the theoretically computed values further affirming the distorted square pyramidal geometry for the vanadyl(IV) complex. Cyclic voltammetry revealed a metal centered single-electron oxidation-reduction response for VO(IV)/VO(V) couple. The antioxidant activity of the vanadium(IV)-complex vis-à-vis the antibiotic has been assessed by 1,1-diphenyl-2-picrylhydrazyl (DPPH) method. The vanadium complex showed comparatively better radical scavenging ability compared to the antibiotic cefuroxime. The antimicrobial activity of the compound has been assayed for five different microbial strains using minimum inhibitory concentration (MIC) method. Immunomodulatory studies carried out using phagocytosis index, myeloperoxidase release and cytokine assay indicated the vanadium(IV)-complex to be immunosuppressant. The cytotoxicity of the compound was evaluated by MTT (3-(4, 5-dimethyl thiazol-2-yl)-2, 5-diphenyl tetrazolium bromide) reduction assay. PMID:25982330

  1. Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex.

    OpenAIRE

    Myshkin, Eugene; Leontis, Neocles B.; Bullerjahn, George S

    2002-01-01

    We have used several docking algorithms (GRAMM, FTDOCK, DOT, AUTODOCK) to examine protein-protein interactions between plastocyanin (Pc)/photosystem I (PSI) in the electron transfer reaction. Because of the large size and complexity of this system, it is faster and easier to use computer simulations than conduct x-ray crystallography or nuclear magnetic resonance experiments. The main criterion for complex selection was the distance between the copper ion of Pc and the P700 chlorophyll specia...

  2. Synthesis, anticancer activity and molecular docking study of Schiff base complexes containing thiazole moiety

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    Mokhles M. Abd-Elzaher

    2016-03-01

    Full Text Available A Schiff base ligand 1 was prepared from condensation of salicyaldehyde with 2-amino-4-phenyl-5-methyl thiazole. The ligand forms complexes with CoII, NiII, CuII, and ZnII in good yield. The synthesized compounds were characterized by elemental analysis, magnetic susceptibility, molar conductance, infrared spectra, 1H and 13C NMR, mass, electronic absorption and ESR spectroscopy. The anticancer activity of the synthesized compounds was studied against different human tumor cell lines: breast cancer MCF-7, liver cancer HepG2, lung carcinoma A549 and colorectal cancer HCT116 in comparison with the activity of doxorubicin as a reference drug. The study showed that ZnII complex showed potent inhibition against human TRK in the four cell lines (HepG2, MCF7, A549, HCT116 by the ratio 80, 70, 61 and 64% respectively as compared to the inhibition in the untreated cells. Moreover, the molecular docking into TRK (PDB: 1t46 was done for the optimization of the aforementioned compounds as potential TRK inhibitors.

  3. Involvement of complexin 2 in docking, locking and unlocking of different SNARE complexes during sperm capacitation and induced acrosomal exocytosis.

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    Pei-Shiue J Tsai

    Full Text Available Acrosomal exocytosis (AE is an intracellular multipoint fusion reaction of the sperm plasma membrane (PM with the outer acrosomal membrane (OAM. This unique exocytotic event enables the penetration of the sperm through the zona pellucida of the oocyte. We previously observed a stable docking of OAM to the PM brought about by the formation of the trans-SNARE complex (syntaxin 1B, SNAP 23 and VAMP 3. By using electron microscopy, immunochemistry and immunofluorescence techniques in combination with functional studies and proteomic approaches, we here demonstrate that calcium ionophore-induced AE results in the formation of unilamellar hybrid membrane vesicles containing a mixture of components originating from the two fused membranes. These mixed vesicles (MV do not contain the earlier reported trimeric SNARE complex but instead possess a novel trimeric SNARE complex that contained syntaxin 3, SNAP 23 and VAMP 2, with an additional SNARE interacting protein, complexin 2. Our data indicate that the earlier reported raft and capacitation-dependent docking phenomenon between the PM and OAM allows a specific rearrangement of molecules between the two docked membranes and is involved in (1 recruiting SNAREs and complexin 2 in the newly formed lipid-ordered microdomains, (2 the assembly of a fusion-driving SNARE complex which executes Ca(2+-dependent AE, (3 the disassembly of the earlier reported docking SNARE complex, (4 the recruitment of secondary zona binding proteins at the zona interacting sperm surface. The possibility to study separate and dynamic interactions between SNARE proteins, complexin and Ca(2+ which are all involved in AE make sperm an ideal model for studying exocytosis.

  4. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

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    Aguilera Longendri

    2007-08-01

    Full Text Available Abstract Background The number of algorithms available to predict ligand-protein interactions is large and ever-increasing. The number of test cases used to validate these methods is usually small and problem dependent. Recently, several databases have been released for further understanding of protein-ligand interactions, having the Protein Data Bank as backend support. Nevertheless, it appears to be difficult to test docking methods on a large variety of complexes. In this paper we report the development of a new database of protein-ligand complexes tailored for testing of docking algorithms. Methods Using a new definition of molecular contact, small ligands contained in the 2005 PDB edition were identified and processed. The database was enriched in molecular properties. In particular, an automated typing of ligand atoms was performed. A filtering procedure was applied to select a non-redundant dataset of complexes. Data mining was performed to obtain information on the frequencies of different types of atomic contacts. Docking simulations were run with the program DOCK. Results We compiled a large database of small ligand-protein complexes, enriched with different calculated properties, that currently contains more than 6000 non-redundant structures. As an example to demonstrate the value of the new database, we derived a new set of chemical matching rules to be used in the context of the program DOCK, based on contact frequencies between ligand atoms and points representing the protein surface, and proved their enhanced efficiency with respect to the default set of rules included in that program. Conclusion The new database constitutes a valuable resource for the development of knowledge-based docking algorithms and for testing docking programs on large sets of protein-ligand complexes. The new chemical matching rules proposed in this work significantly increase the success rate in DOCKing simulations. The database developed in this work is

  5. Docking Design of Self-Reconfigurable Robot

    OpenAIRE

    Fei, Yanqiong

    2011-01-01

    Docking design of self‐reconfigurable robots is studied. Firstly, the self‐reconfigurable robot is presented. Its basic module is designed, which is composed of a central cube and six rotary arms. Then, the novel docking mechanism of each module is designed. It is critical for the self‐reconfigurable robot to discard any faulty modules for the self‐repairing actions. The docking process is analyzed with the geometric method. The docking forces between two modules are d...

  6. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

    OpenAIRE

    Morris, Garrett M.; Huey, Ruth; Lindstrom, William; Sanner, Michel F.; Belew, Richard K.; Goodsell, David S.; Olson, Arthur J.

    2009-01-01

    We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently-bound ligands, using both a grid-based docking method and a modification of the...

  7. HIV-1 Nef Binds the DOCK2-ELMO1 Complex to Activate Rac and Inhibit Lymphocyte Chemotaxis

    Directory of Open Access Journals (Sweden)

    Janardhan Ajit

    2004-01-01

    Full Text Available The infectious cycle of primate lentiviruses is intimately linked to interactions between cells of the immune system. Nef, a potent virulence factor, alters cellular environments to increase lentiviral replication in the host, yet the mechanisms underlying these effects have remained elusive. Since Nef likely functions as an adaptor protein, we exploited a proteomic approach to directly identify molecules that Nef targets to subvert the signaling machinery in T cells. We purified to near homogeneity a major Nef-associated protein complex from T cells and identified by mass spectroscopy its subunits as DOCK2-ELMO1, a key activator of Rac in antigen- and chemokine-initiated signaling pathways, and Rac. We show that Nef activates Rac in T cell lines and in primary T cells following infection with HIV-1 in the absence of antigenic stimuli. Nef activates Rac by binding the DOCK2-ELMO1 complex, and this interaction is linked to the abilities of Nef to inhibit chemotaxis and promote T cell activation. Our data indicate that Nef targets a critical switch that regulates Rac GTPases downstream of chemokine- and antigen-initiated signaling pathways. This interaction enables Nef to influence multiple aspects of T cell function and thus provides an important mechanism by which Nef impacts pathogenesis by primate lentiviruses.

  8. On the chains of star complexes and superclouds in spiral arms

    CERN Document Server

    Efremov, Yuri N

    2010-01-01

    The relation is studied between occurrence of a regular chain of star complexes and superclouds in a spiral arm, and other properties of the latter. A regular string of star complexes is located in the north-western arm of M31; they have about the same size 0.6 kpc with spacing of 1.1 kpc. Within the same arm segment the regular magnetic field with the wavelength of 2.3 kpc was found by Beck et al. (1989). We noted that this wavelength is twice as large as the spacing between complexes and suggested that they were formed in result of magneto-gravitational instability developed along the arm. In this NW arm, star complexes are located inside the gas-dust lane, whilst in the south-western arm of M31 the gas-dust lane is upstream of the bright and uniform stellar arm. Earlier, evidence for the age gradient has been found in the SW arm. All these are signatures of a spiral shock, which may be associated with unusually large (for M31) pitch-angle of this SW arm segment. Such a shock may prevent the formation of th...

  9. Identify Inhibitors on DAPK2 and ELMO1-DOCK2 Complex via Virtual Screening

    OpenAIRE

    Wu, Meixin

    2016-01-01

    Death associated protein kinase 2 (DAPK2) is a serine threonine kinase with 370 amino acid residues, whose structure is highly conserved with the other members in the death associated protein kinase (DAPK) family. To find out the inhibitors with high specificity to DAPK2, structural based virtual screening was carried out. According to the results of docking, ligand clustering, MM/GBSA analysis and position of ligands in the DAPK2 binding pocket, it can be concluded that DA7, whose binding af...

  10. The C-terminal polyproline-containing region of ELMO contributes to an increase in the life-time of the ELMO-DOCK complex.

    Science.gov (United States)

    Sévajol, Marion; Reiser, Jean-Baptiste; Chouquet, Anne; Pérard, Julien; Ayala, Isabel; Gans, Pierre; Kleman, Jean-Philippe; Housset, Dominique

    2012-03-01

    The eukaryotic Engulfment and CellMotility (ELMO) proteins form an evolutionary conserved family of key regulators which play a central role in Rho-dependent biological processes such as engulfment and cell motility/migration. ELMO proteins interact with a subset of Downstream of Crk (DOCK) family members, a new type of guanine exchange factors (GEF) for Rac and cdc42 GTPases. The physiological function of DOCK is to facilitate actin remodeling, a process which occurs only in presence of ELMO. Several studies have determined that the last 200 C-terminal residues of ELMO1 and the first 180 N-terminal residues of DOCK180 are responsible for the ELMO-DOCK interaction. However, the precise role of the different domains and motifs identified in these regions has remained elusive. Divergent functional, biochemical and structural data have been reported regarding the contribution of the C-terminal end of ELMO, comprising its polyproline motif, and of the DOCK SH3 domain. In the present study, we have investigated the contribution of the C-terminal end of ELMO1 to the interaction between ELMO1 and the SH3 domain of DOCK180 using nuclear magnetic resonance spectroscopy and surface plasmon resonance. Our data presented here demonstrate the ability of the SH3 domain of DOCK180 to interact with ELMO1, regardless of the presence of the polyproline-containing C-terminal end. However, the presence of the polyproline region leads to a significant increase in the half-life of the ELMO1-DOCK180 complex, along with a moderate increase on the affinity. PMID:22177965

  11. Synthesis, DNA-binding, cytotoxicity, photo cleavage, antimicrobial and docking studies of Ru(II) polypyridyl complexes.

    Science.gov (United States)

    Srishailam, A; Kumar, Yata Praveen; Gabra, Nazar M D; Reddy, P Venkat; Deepika, N; Veerababu, Nageti; Satyanarayana, S

    2013-09-01

    Three Ruthenium(II) polypyridine complexes, [Ru(phen)2(mipc)](2+)(1), [Ru(bpy)2(mipc)](2+) (2) and [Ru(dmb)2(mipc)](2+)(3) [mipc = 2-(6-methyl-3-(1H-imidazo[4, 5-f][1,10]-phenanthroline-2-yl)-4H-chromene-4-one, phen = 1,10-phenanthroline,bpy = 2, 2'bipyridine,dmb = 4, 4'-dimethyl-2, 2'-bipyridine] have been synthesized and characterized by elemental analysis, IR, UV-Vis, (1)H& (13)C NMR and mass spectra. The DNA-binding properties of the Ruthenium(II) complexes were investigated by spectrophotometric methods, viscosity measurements and light switch studies. These three complexes have been focused on photo activated cleavage studies with pBR-322 and antimicrobial studies. Experimental results indicate that the three complexes intercalate into DNA base pairs and follows the order of 1 > 2 > 3 respectively. Molecular docking studies also support the DNA interactions with complexes through hydrogen bonding and vander Waal's interactions. Cytotoxicity studies with Hela cell lines has been revealing about anti tumor activity of these complexes. PMID:23553642

  12. Synthesis, cytotoxicity assessment, and interaction and docking of novel palladium(II) complexes of imidazole derivatives with human serum albumin.

    Science.gov (United States)

    Eslami Moghadam, Mahboube; Divsalar, Adeleh; Abolhosseini Shahrnoy, Abdolghafar; Saboury, Ali Akbar

    2016-08-01

    Imidazole analogs are the agents that attract both bioinorganic chemist and drug designer. Numerous methods have been proposed for synthesis of imidazole derivatives. In this study, a series of heterocyclic system with p-conjugated system such as 2-aryl-imidazo[4,5-f][1,10]phenanthroline analogs were synthesized. Then, three new palladium(II) complexes containing 2-(Furan-2-yl)-1H-Imidazo[4,5-f][1,10]Phenanthroline (FIP) and 2-(thiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (TIP) ligands were synthesized. The structures of the compounds, [Pd(Phen)(TIP)](NO3)2, [Pd(Phen)(FIP)](NO3)2, and [Pd(FIP)2]Cl were determined by spectroscopic methods and elemental analysis. Biological activity of the complexes synthesized was assessed against chronic myelogenous leukemia cell line, K562. Also, the interactions of human serum albumin with complexes were investigated using isothermal titration in the Tris buffer, pH 7.4. According to the results obtained, it was found that there is a set of six binding sites for these complexes on HSA with positive cooperativity in the binding process. Docking technique was also applied to confirm the experimental results. The results showed that smaller complexes have higher interaction affinity. PMID:26338667

  13. A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints

    International Nuclear Information System (INIS)

    A simple and reliable approach for docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel representation for an attractive potential between mapped interaction surfaces is described. Unambiguous assignments of very sparse intermolecular NOEs are obtained using a reverse labeling strategy in which one the components is fully deuterated with the exception of selective protonation of the δ-methyl groups of isoleucine, while the other component is uniformly 13C-labeled. This labeling strategy can be readily extended to selective protonation of Ala, Leu, Val or Met. The attractive potential is described by a 'reduced' radius of gyration potential applied specifically to a subset of interfacial residues (those with an accessible surface area ≥ 50% in the free proteins) that have been delineated by chemical shift perturbation. Docking is achieved by rigid body minimization on the basis of a target function comprising the sparse NOE distance restraints, a van der Waals repulsion potential and the 'reduced' radius of gyration potential. The method is demonstrated for two protein-protein complexes (EIN-HPr and IIAGlc-HPr) from the bacterial phosphotransferase system. In both cases, starting from 100 different random orientations of the X-ray structures of the free proteins, 100% convergence is achieved to a single cluster (with near identical atomic positions) with an overall backbone accuracy of ∼2 A. The approach described is not limited to NMR, since interfaces can also be mapped by alanine scanning mutagenesis, and sparse intermolecular distance restraints can be derived from double cycle mutagenesis, cross-linking combined with mass spectrometry, or fluorescence energy transfer

  14. Synthesis, characterization, DNA binding studies, photocleavage, cytotoxicity and docking studies of ruthenium(II) light switch complexes.

    Science.gov (United States)

    Gabra, Nazar Mohammed; Mustafa, Bakheit; Kumar, Yata Praveen; Devi, C Shobha; Srishailam, A; Reddy, P Venkat; Reddy, Kotha Laxma; Satyanarayana, S

    2014-01-01

    A new ligand 3-(1H-imidazo[4,5-f][1,10]phenanthrolin-2yl)phenylboronic acid and its (IPPBA) three ruthenium(II) complexes [Ru(phen)2(IPPBA)](ClO4)2 (1), [Ru(bpy)2(IPPBA)](ClO4)2 (2) and [Ru(dmb)2(IPPBA)](ClO4)2 (3) have been synthesized and characterized by elemental analysis, UV/VIS, IR, (1)H-NMR,(13)C-NMR and mass spectra. The binding behaviors of the three complexes to calf thymus DNA were investigated by absorption spectra, emission spectroscopy, viscosity measurements, thermal denaturation and photoactivated cleavage. The DNA-binding constants for complexes 1, 2 and 3 have been determined to be 7.9 × 10(5) M(-1), 6.7 × 10(5) M(-1) and 2.9 × 10(5) M(-1). The results suggest that these complexes bound to double-stranded DNA in an intercalation mode. Upon irradiation at 365 nm, three ruthenium complexes were found to promote the cleavage of plasmid pBR322 DNA from super coiled form І to nicked form ІІ. Further in the presence of Co(2+), the emission of DNA-Ru(ΙΙ) complexes can be quenched. And when EDTA was added, the emission was recovered. The experimental results show that all three complexes exhibited the "on-off-on" properties of molecular "light switch". The highest Cytotoxicity potential of the complex1 was observed on the Human alveolar adenocarcinoma (A549) cell line. Good agreement was generally found between the spectroscopic techniques and molecular docked model which provides further evidence of groove binding. PMID:23982735

  15. PREPARATION AND CHARACTERIZATION OF INCLUSION COMPLEXES OF TWO-ARM LINEAR AND FOUR-ARM STAR-SHAPED POLY(ε-CAPROLACTONE)S WITH α-CYCLODEXTRIN

    Institute of Scientific and Technical Information of China (English)

    Lu Wang; Jing-liang Wang; Chang-ming Dong

    2006-01-01

    Both four-arm star-shaped poly(ε-caprolactone) (4sPCL) and two-arm linear PCL (2LPCL) were synthesized and their inclusion complexation with α-cyclodextrin (α-CD) were studied. The inclusion complexes (ICs) formed between the PCL polymers and α-CD were characterized by 1H-NMR, DSC, TGA, WAXD, and FT-IR, respectively. Both branch arm number and molecular weight of the PCL polymers have apparent effect on the stoichiometry (CL:CD, mol:mol) of these ICs. All these analytical results indicate that the branch arms of the PCL polymers are incorporated into the hydrophobicα-CD cavities and their original crystalline properties are completely suppressed. Moreover, the inclusion complexation between two-arm linear or four-arm star-shaped PCL polymers and α-CD not only enhances the thermal stability of the guest PCL polymers but also improves that of α-CD.

  16. Armes

    OpenAIRE

    Camps, G.; Chenorkian, R.; Lhote, H.

    2013-01-01

    Préhistoire (G. Camps) Les armes des Paléoberbères de la Préhistoire ne présentent guère d’originalité mais à la documentation archéologique provenant de fouilles s’ajoute, en Afrique du Nord et au Sahara, une documentation iconographique d’une grande richesse que ne possèdent pas les autres pays riverains du bassin occidental de la Méditerranée. Durant les temps paléolithiques, les hommes qui occupèrent le Maghreb et le Sahara utilisèrent, en plus des outils et armes connus ailleurs ; biface...

  17. Transformation of the fourth power block of the Chernobyl atomic power station into a ecologically safe system by a dock-caisson technological complex

    International Nuclear Information System (INIS)

    The designers of the technical solution do not doubt that it is possible to transform the fourth power block of the Chernobyl APS into an ecologically safe system by help of Dock-Caisson technological complex. Application of the Dock-Caisson allows to make the operations of phases 1 and 2 of the Shelter installation transformation at the same time, i.e. to make the installation stabilization and preparation to radioactive wastes extraction simultaneously. By completion of first two phases the conditions are created for instant beginning of phase 3, i.e. disassembling of the content of the crashed power block

  18. DockingShop: A Tool for Interactive Molecular Docking

    OpenAIRE

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-01-01

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. DockingShop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. O...

  19. How proteins get in touch: Interface prediction and docking of protein complexes

    NARCIS (Netherlands)

    de Vries, S.J.

    2009-01-01

    Proteins are the wheels and mill stones of the complex machinery that underlies human life. In carrying out their functions, proteins work in close association with other proteins, forming protein complexes. A huge network of protein-protein interactions enables the cell to respond quickly to change

  20. Determination of non-covalent docking by IR spectroscopy of cold gas-phase complexes

    OpenAIRE

    Garand, Etienne; Kamrath, Michael Z.; Jordan, Peter A.; Wolk, Arron B.; Leavitt, Christopher M.; Mccoy, Anne B.; Miller, Scott J.; Johnson, Mark A.

    2012-01-01

    Multi-dentate, non-covalent interactions between small molecules and biopolymer fragments are central to processes ranging from drug action to selective catalysis. We present a versatile and sensitive spectroscopic probe of functional groups engaged in hydrogen bonding in such contexts. This involves measurement of the frequency changes in specific covalent bonds upon complex formation, information drawn from otherwise transient complexes that have been extracted from solution and conformatio...

  1. AN OVERVIEW ON MOLECULAR DOCKING

    Directory of Open Access Journals (Sweden)

    Gaba Monika

    2010-06-01

    Full Text Available Molecular Docking is the computational modeling of the structure of complexes formed by two or more interacting molecules. The goal of molecular docking is the prediction of the three dimensional structures of interest. Docking itself only produces plausible candidate structures. These candidates are ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. The state of the art of various computational aspects of molecular docking based virtual screening of database of small molecules is presented. This review encompasses molecular docking approaches, different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Limitations of current technologies as well as future prospects are also presented

  2. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René

    2003-01-01

    Molecular docking of biomolecules is becoming an increasingly important part in the process of developing new drugs, as well as searching compound databases for promising drug candidates. The docking of ligands to proteins can be formulated as an optimization problem where the task is to find the...... most favorable energetic conformation among the large space of possible protein-ligand complexes. Stochastic search methods, such as evolutionary algorithms (EAs), can be used to sample large search spaces effectively and is one of the preferred methods for flexible ligand docking. The differential...... evolution algorithm (DE) is applied to the docking problem using the AutoDock program. The introduced DockDE algorithm is compared with the Lamarckian GA (LGA) provided with AutoDock, and the DockEA previously found to outperform the LGA. The comparison is performed on a suite of six commonly used docking...

  3. Molecular docking study on the α3β2 neuronal nicotinic acetylcholine receptor complexed with α-Conotoxin GIC

    Directory of Open Access Journals (Sweden)

    Chewook Lee

    2012-05-01

    Full Text Available Nicotinic acetylcholine receptors (nAChRs are a diverse familyof homo- or heteropentameric ligand-gated ion channels.Understanding the physiological role of each nAChR subtypeand the key residues responsible for normal and pathologicalstates is important. α-Conotoxin neuropeptides are highly selectiveprobes capable of discriminating different subtypes ofnAChRs. In this study, we performed homology modeling togenerate the neuronal α3, β2 and β4 subunits using the x-raystructure of the α1 subunit as a template. The structures of theextracellular domains containing ligand binding sites in theα3β2 and α3β4 nAChR subtypes were constructed using MDsimulations and ligand docking processes in their free and ligand-bound states using α-conotoxin GIC, which exhibited thehighest α3β2 vs. α3β4 discrimination ratio. The results providea reasonable structural basis for such a discriminatoryability, supporting the idea that the present strategy can beused for future investigations on nAChR-ligand complexes.[BMB reports 2012; 45(5: 275-280

  4. The Development of Bispecific Hexavalent Antibodies as a Novel Class of DOCK-AND-LOCKTM (DNLTM Complexes

    Directory of Open Access Journals (Sweden)

    Chien-Hsing Chang

    2013-05-01

    Full Text Available The DOCK-AND-LOCKTM (DNLTM method provides a modular approach to develop multivalent, multifunctional complexes of defined structures, of which bispecific hexavalent antibodies (bsHexAbs are prominent examples with potential applications in targeted therapy for malignant, autoimmune, and infectious diseases. Currently, bsHexAbs are constructed by derivatizing a divalent IgG, at the carboxyl termini of either the heavy chain (the CH3-format or the light chain (the Ck-format, to contain two stabilized dimers of Fab having a different specificity from the IgG. In this review, we briefly outline the features of the DNLTM method and describe key aspects of bsHexAbs examined with diverse preclinical studies, which include binding affinity to target cells, induction of signaling pathways, effector functions, serum stability, pharmacokinetics, and antitumor activity in human tumor xenograft models. Our findings favor the selection of the CK- over the CH3-format for further exploration of bsHexAbs in clinical trials.

  5. DockingShop: A Tool for Interactive Molecular Docking

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  6. Elmo1 inhibits ubiquitylation of Dock180.

    Science.gov (United States)

    Makino, Yoshinori; Tsuda, Masumi; Ichihara, Shin; Watanabe, Takuya; Sakai, Mieko; Sawa, Hirofumi; Nagashima, Kazuo; Hatakeyama, Shigetsugu; Tanaka, Shinya

    2006-03-01

    Dock180, a member of the CDM family of proteins, plays roles in biological processes such as phagocytosis and motility through its association with the signalling adaptor protein Crk. Recently, the complex formation between Dock180 and Elmo1 was reported to function as a bipartite guanine nucleotide exchange factor for Rac. In this study, we demonstrated that the amount of Dock180 increased when Elmo1 was co-expressed. Dock180 was found to be ubiquitylated and Dock180 protein levels could be augmented by treatment with proteasome inhibitor. The ubiquitylation of Dock180 was enhanced by epidermal growth factor (EGF), Crk and adhesion-dependent signals. Furthermore, Elmo1 inhibited ubiquitylation of Dock180, resulting in the increase in Dock180 levels. The Elmo1 mutant Delta531, which encompasses amino acids required for Dock180 binding, preserved the inhibitory effects on ubiquitylation of Dock180. Upon EGF stimulation, both Dock180 and ubiquitin were demonstrated to translocate to the cell periphery by immunofluorescence, and we found ubiquitylation of Dock180 and its inhibition by Elmo1 to occur in cellular membrane fractions by in vivo ubiquitylation assay. These data suggest that Dock180 is ubiquitylated on the plasma membrane, and also that Elmo1 functions as an inhibitor of ubiquitylation of Dock180. Therefore, an ubiquitin-proteasome-dependent protein degradation mechanism might contribute to the local activation of Rac on the plasma membrane. PMID:16495483

  7. α-Cyclodextrin dimer complexes of dopamine and levodopa derivatives to assess drug delivery to the central nervous system: ADME and molecular docking studies

    OpenAIRE

    Shityakov, Sergey; Broscheit, Jens; Förster, Carola

    2012-01-01

    This paper attempts to predict and emphasize molecular interactions of dopamine, levodopa, and their derivatives (Dopimid compounds) containing 2-phenyl-imidazopyridine moiety with the α-cyclodextrin dimer in order to assess and improve drug delivery to the central nervous system. The molecular docking method is used to determine the energetic profiles, hydrogen bond formation, and hydrophobic effect of 14 host–guest complexes. The results show that the “chemical branching” represented by add...

  8. The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism.

    Directory of Open Access Journals (Sweden)

    Gergő Gógl

    2015-05-01

    Full Text Available Eukaryotic cells commonly use protein kinases in signaling systems that relay information and control a wide range of processes. These enzymes have a fundamentally similar structure, but achieve functional diversity through variable regions that determine how the catalytic core is activated and recruited to phosphorylation targets. "Hippo" pathways are ancient protein kinase signaling systems that control cell proliferation and morphogenesis; the NDR/LATS family protein kinases, which associate with "Mob" coactivator proteins, are central but incompletely understood components of these pathways. Here we describe the crystal structure of budding yeast Cbk1-Mob2, to our knowledge the first of an NDR/LATS kinase-Mob complex. It shows a novel coactivator-organized activation region that may be unique to NDR/LATS kinases, in which a key regulatory motif apparently shifts from an inactive binding mode to an active one upon phosphorylation. We also provide a structural basis for a substrate docking mechanism previously unknown in AGC family kinases, and show that docking interaction provides robustness to Cbk1's regulation of its two known in vivo substrates. Co-evolution of docking motifs and phosphorylation consensus sites strongly indicates that a protein is an in vivo regulatory target of this hippo pathway, and predicts a new group of high-confidence Cbk1 substrates that function at sites of cytokinesis and cell growth. Moreover, docking peptides arise in unstructured regions of proteins that are probably already kinase substrates, suggesting a broad sequential model for adaptive acquisition of kinase docking in rapidly evolving intrinsically disordered polypeptides.

  9. Surflex-Dock: Docking benchmarks and real-world application

    OpenAIRE

    Spitzer, R.; Jain, AN

    2012-01-01

    Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is r...

  10. Hydrogenation of esters catalyzed by ruthenium PN3-Pincer complexes containing an aminophosphine arm

    KAUST Repository

    Chen, Tao

    2014-08-11

    Hydrogenation of esters under mild conditions was achieved using air-stable ruthenium PN3-pincer complexes containing an aminophosphine arm. High efficiency was achieved even in the presence of water. DFT studies suggest a bimolecular proton shuttle mechanism which allows H2 to be activated by the relatively stable catalyst with a reasonably low transition state barrier. © 2014 American Chemical Society.

  11.  α-Cyclodextrin dimer complexes of dopamine and levodopa derivatives to assess drug delivery to the central nervous system: ADME and molecular docking studies

    Directory of Open Access Journals (Sweden)

    Shityakov S

    2012-06-01

    Full Text Available Sergey Shityakov, Jens Broscheit, Carola FörsterDepartment of Anesthesiology and Critical Care, University of Würzburg, Würzburg, GermanyAbstract: This paper attempts to predict and emphasize molecular interactions of dopamine, levodopa, and their derivatives (Dopimid compounds containing 2-phenyl-imidazopyridine moiety with the α-cyclodextrin dimer in order to assess and improve drug delivery to the central nervous system. The molecular docking method is used to determine the energetic profiles, hydrogen bond formation, and hydrophobic effect of 14 host–guest complexes. The results show that the “chemical branching” represented by additional ethyl-acetate residue is energetically unfavorable and promotes a conformational shift due to the high root mean square deviation levels. This phenomenon is characterized by a low number of H-bonds and a significant decrease of the host–guest hydrophobic potential surface. Finally, the overall docking procedure presents a powerful rationale for screening and analyzing various sets of promising drug-like chemical compounds in the fields of supramolecular chemistry, molecular sensing, synthetic receptors, and nanobiotechnology.Keywords: dopamine, levodopa, Dopimid compounds, α-CD dimer, molecular docking, complexation

  12. Synthesis, molecular docking and evaluation of antifungal activity of Ni(II),Co(II) and Cu(II) complexes of porphyrin core macromolecular ligand.

    Science.gov (United States)

    Singh, Urvashi; Malla, Ali Mohammad; Bhat, Imtiyaz Ahmad; Ahmad, Ajaz; Bukhari, Mohd Nadeem; Bhat, Sneha; Anayutullah, Syed; Hashmi, Athar Adil

    2016-04-01

    Porphyrin core dendrimeric ligand (L) was synthesized by Rothemund synthetic route in which p-hydroxy benzaldehyde and pyrrole were fused together. The prepared ligand was complexed with Ni(II), Cu(II) and Co(II) ions, separately. Both the ligand and its complexes were characterized by elemental analysis and spectroscopic studies (FT-IR, UV-Vis, (1)HNMR). Square planar geometries were proposed for Cu(II), Ni(II) and Co(II) ions in cobalt, Nickel and copper complexes, respectively on the basis of UV-Vis spectroscopic data. The ligand and its complex were screened on Candida albicans (ATCC 10231), Aspergillus fumigatus (ATCC 1022), Trichophyton mentagrophytes (ATCC 9533) and Pencillium marneffei by determining MICs and inhibition zones. The activity of the ligand and its complexes was found to be in the order: CuL ˃ CoL ≈ NiL ˃ L. Detection of DNA damage at the level of the individual eukaryotic cell was observed by commet assay. Molecular docking technique was used to understand the ligand-DNA interactions. From docking experiment, we conclude that copper complex interacts more strongly than rest two. PMID:26911647

  13. Modeling holo-ACP:DH and holo-ACP:KR complexes of modular polyketide synthases: a docking and molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Anand Swadha

    2012-05-01

    Full Text Available Abstract Background Modular polyketide synthases are multifunctional megasynthases which biosynthesize a variety of secondary metabolites using various combinations of dehydratase (DH, ketoreductase (KR and enoyl-reductase (ER domains. During the catalysis of various reductive steps these domains act on a substrate moiety which is covalently attached to the phosphopantetheine (P-pant group of the holo-Acyl Carrier Protein (holo-ACP domain, thus necessitating the formation of holo-ACP:DH and holo-ACP:KR complexes. Even though three dimensional structures are available for DH, KR and ACP domains, no structures are available for DH or KR domains in complex with ACP or substrate moieties. Since Ser of holo-ACP is covalently attached to a large phosphopantetheine group, obtaining complexes involving holo-ACP by standard protein-protein docking has been a difficult task. Results We have modeled the holo-ACP:DH and holo-ACP:KR complexes for identifying specific residues on DH and KR domains which are involved in interaction with ACP, phosphopantetheine and substrate moiety. A novel combination of protein-protein and protein-ligand docking has been used to first model complexes involving apo-ACP and then dock the phosphopantetheine and substrate moieties using covalent connectivity between ACP, phosphopantetheine and substrate moiety as constraints. The holo-ACP:DH and holo-ACP:KR complexes obtained from docking have been further refined by restraint free explicit solvent MD simulations to incorporate effects of ligand and receptor flexibilities. The results from 50 ns MD simulations reveal that substrate enters into a deep tunnel in DH domain while in case of KR domain the substrate binds a shallow surface exposed cavity. Interestingly, in case of DH domain the predicted binding site overlapped with the binding site in the inhibitor bound crystal structure of FabZ, the DH domain from E.Coli FAS. In case of KR domain, the substrate binding site

  14. Customizing Scoring Functions for Docking

    OpenAIRE

    Pham, Tuan A.; Jain, Ajay N.

    2008-01-01

    Empirical scoring functions used in protein-ligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function’s training towards a particular application, such as screening enrichment. The approach combi...

  15. Free Energy Calculation of Docking Structure of Azurin(I)-Cytochrome c551(III) Complex Systems by Using the Energetic Representation

    Science.gov (United States)

    Nishikawa, Keigo; Yamamoto, Tetsunori; Sugiyama, Ayumu; Purqon, Acep; Mizukami, Taku; Shimahara, Hideto; Nagao, Hidemi; Nishikawa, Kiyoshi

    2008-02-01

    We investigate the docking stability of Azurin(I)—Cytochrome C551(III) complex by molecular dynamic simulations. The charge distribution around the active sites for Azurin(I) and Cytochrome C551(III) is estimated by quantum chemical calculation to simulate the complex system by molecular dynamic simulations. We estimete some physical properties such as the root square mean deviation, distance between iron ion in active site of Cytochrome C551(III) and copper ion in active site of Azurin(I), the dynamical cross-correlation map and free energy in the energetic representation. We discuss the stability of the complex system of Azurin(I)—Cytochrome C551(III) from these properties.

  16. Binding affinities of Schiff base Fe(II) complex with BSA and calf-thymus DNA: Spectroscopic investigations and molecular docking analysis.

    Science.gov (United States)

    Rudra, Suparna; Dasmandal, Somnath; Patra, Chiranjit; Kundu, Arjama; Mahapatra, Ambikesh

    2016-09-01

    The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb=(7.6±0.21)×10(5)) between complex and protein have been obtained at 298K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2±0.11)×10(6)M(-1). Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules. PMID:27214273

  17. Synthesis, characterization and studies on antioxidant and molecular docking of metal complexes of 1-(benzo[d]thiazol-2-yl)thiourea

    Indian Academy of Sciences (India)

    Harinath Yapati; Subba Rao Devineni; Suresh Chirumamilla; Seshaiah Kalluru

    2016-01-01

    In the present study, a new thiourea derivative bearing benzothiazole ligand, 1-(benzo[d]thiazol-2-yl)thiourea (btt) and its ternary metal (Cu(II), Co(II) and Ni(II)) complexes were synthesized. The structural characterization was carried out by micro analysis, IR, 1H-NMR, EPR, UV-Visible spectral analyses, molar conductance and thermal analysis studies. Spectral studies of complexes revealed that the metal complexes have distorted octahedral geometry. Molecular modelling study was performed to evaluate the recognition of target compounds at the 3MNG binding pocket. The docking results revealed that copper complex selectively binds to the crucial amino acid residues in the active site of 3MNG. The in vitro antioxidant activity of the ligand and its metal complexes was assayed by radical scavenging activity (DPPH, H2O2 and NO) and ferric reducing antioxidant power (FRAP) methods. The ligand showed moderate antioxidant activity whereas the metal complexes exhibited better antioxidant activity than that of the ligand. The results of the four methods proved that the copper complex is the most potent antioxidant among all the tested compounds.

  18. Synthesis, crystal structures, molecular docking, and in vitro biological activities evaluation of transition metal complexes with 4-(3,4-dichlorophenyl) piperazine-1-carboxylic acid

    Science.gov (United States)

    Chen, Zhi-Jian; Chen, Ya-Na; Xu, Chun-Na; Zhao, Shan-Shan; Cao, Qi-Yue; Qian, Shao-Song; Qin, Jie; Zhu, Hai-Liang

    2016-08-01

    Three novel mononuclear complexes, [MⅡ(L)2·2H2O], (M = Cu, Ni or Cd; HL = 4-(3,4-dichlorophenyl)piperazine-1-carboxylic acid)were synthesized and structurally determined by single-crystal X-ray diffraction. Molecular docking study preliminarily revealed that complex 1 had potential urease inhibitory activity. In accordance with the result of calculation, in vitro tests of the inhibitory activities of complexes 1-3 against jack bean urease showed complex 1 (IC50 = 8.17 ± 0.91 μM) had better inhibitory activities than the positive reference acetohydroxamic acid (AHA) (IC50 = 26.99 ± 1.43 μM), while complexes 2 and 3 showed no inhibitory activities., kinetics study was carried out to explore the mechanism of the inhibiting of the enzyme, and the result indicated that complex 1 was a competitive inhibitor of urease. Albumin binding experiment and in vitro toxicity evaluation of complex 1 were implemented to explore its Pharmacological properties.

  19. Newer mixed ligand Schiff base complexes from aquo-N-(2‧-hydroxy acetophenone) glycinatocopper(II) as synthon: DFT, antimicrobial activity and molecular docking study

    Science.gov (United States)

    Pramanik, Harun A. R.; Das, Dharitri; Paul, Pradip C.; Mondal, Paritosh; Bhattacharjee, Chira R.

    2014-02-01

    Synthesis of a series of newer mixed ligand copper(II) complexes of aminoacid Schiff base of the type [CuL(X)] (L = N-(2‧-hydroxy acetophenone) glycinate, X = imidazole (im) 2, benzimidazole (benz) 3, pyridine (py) 4, hydrazine (hz) 5,8-hydroxyquinoline (8-hq) 6, pyrrolidine (pyrr) 7, piperidine (pip) 8, and nicotinamide (nic) 9) have been accomplished from the interaction of an aquated Schiff base complex, [CuL(H2O)]·H2O, 1 with some selected neutral nitrogen-donor ligands. The copper(II) Schiff base complex, [CuL(H2O)]·H2O, L = N-(2‧-hydroxy acetophenone) glycinate was synthesized from the reaction of glycine and 2‧ hydroxy acetophenone and copper(II) acetate. The compounds were characterised by elemental analysis, spectral, magnetic and thermal studies. The density functional theory calculations were performed using LANL2DZ and 6-311 G(d, p) basis sets with B3LYP correlation functional to ascertain the stable electronic structure, HOMO-LUMO energy gap, chemical hardness and dipole moment of the mixed ligand complexes. A distorted square planar geometry has been conjectured for the complexes. Antibacterial activities of the ligand and its metal complexes have been tested against selected gram-positive and gram-negative strains and correlated with computational docking scores.

  20. Text Mining for Protein Docking.

    Directory of Open Access Journals (Sweden)

    Varsha D Badal

    2015-12-01

    Full Text Available The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking. Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu. The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound

  1. Luminescent Behavior of Ru(II) Polypyridyl Morpholine Complexes, Synthesis, Characterization, DNA, Protein Binding, Sensor Effect of Ions/Solvents and Docking Studies.

    Science.gov (United States)

    Vuradi, Ravi Kumar; Putta, Venkat Reddy; Nancherla, Deepika; Sirasani, Satyanarayana

    2016-03-01

    New three ruthenium (II) polypyridyl complexes [Ru(phen)2mpip](2+)(1) {mpip = 2-(4-morpholinophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline}, (phen = 1,10-Phenanthrolene), [Ru(bpy)2mpip](2+)(2) (bpy = 2,2'bipyridyl), [Ru(dmb)2mpip](2+)(3) (dmb = 4, 4-dimethyl 2, 2'-bipyridine) have been synthesized and characterized by spectral studies IR, UV-vis, (1)H, (13)C-NMR, mass and elemental analysis. The binding properties of these three complexes towards calf-thymus DNA (CT-DNA) have been investigated by UV-Vis spectroscopy, different fluorescence methods and viscosity measurements, indicating that all the complexes bind to CT-DNA by means of intercalation, but with different binding affinities. Sensor effect of ions/solvents and BSA (Bovine Serum Albumin) binding studies of these complexes were also studied. Docking studies also reveals that complexes will bind in between base pairs (Intercalate) of DNA and gives information about the binding strength. PMID:26708008

  2. Side docking of the da Vinci robotic system for radical prostatectomy: advantages over traditional docking.

    Science.gov (United States)

    Cestari, Andrea; Ferrari, Matteo; Zanoni, Matteo; Sangalli, Mattia; Ghezzi, Massimo; Fabbri, Fabio; Sozzi, Francesco; Rigatti, Patrizio

    2015-09-01

    The standard low lithotomic position, used during robot-assisted radical prostatectomy (RARP), with prolonged positioning in stirrups together with steep Trendelenburg may expose the patient to neurapraxia phenomena of the lower limbs and can rarely be used in patients with problems of hip abduction. To overcome these hurdles, we evaluated the clinical benefits of "side docking" (SD) of the da Vinci(®) robotic system in comparison to "traditional docking" (TD). A cohort of 120 patients submitted to RARP were prospectively randomized into two groups by docking approach: SD with the patient supine with lower limbs slightly abducted on the operating table, and TD docking time, intraoperative number of collisions between the robotic arms and postoperative neurological problems in the lower limbs were noted. Descriptive statistics was used to analyze outcomes. Docking time was shorter for the SD group [SD: median 13 min (range 10-18); TD: median 21 min (range 15-34)]. None in the SD group and six of 60 patients (10%) in the TD group suffered from temporary (<30 days) unilateral neurological deficits of the lower limbs. In both groups no collisions between the robotic arms occurred. The SD approach is technically feasible. It does not cause collisions between the robotic arms, and is a reliable method for reducing the setup time of RARP. The supine position of the patient may prevent neurological complications of the lower limbs. Based on these results, SD has become the standard docking technique used by our department. PMID:26531205

  3. Long-Term Effects of Complex Decongestive Therapy in Breast Cancer Patients With Arm Lymphedema After Axillary Dissection

    OpenAIRE

    Hwang, Jung Min; Hwang, Ji Hye; Kim, Tae Won; Lee, Seung Yeol; Chang, Hyun Ju; Chu, In Ho

    2013-01-01

    Objective To investigate the long-term effects of complex decongestive therapy (CDT) on edema reduction in breast cancer-related lymphedema patients after axillary dissection, according to the initial volume of edema. Methods A retrospective review of 57 patients with unilateral arm after an axillary dissection for breast cancer was performed. The patients, treated with two weeks of CDT and self-administered home therapy, were followed for 24 months. Arm volume was serially measured by using ...

  4. Study of the interaction between two newly synthesized cyclometallated platinum (II) complexes and human serum albumin: Spectroscopic characterization and docking simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yousefi, Reza, E-mail: ryousefi@shirazu.ac.ir [Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Mohammadi, Roghayeh [Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Taheri-Kafrani, Asghar [Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Bagher Shahsavani, Mohammad [Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Dadkhah Aseman, Marzieh; Masoud Nabavizadeh, S.; Rashidi, Mehdi [Department of Chemistry, College of Sciences, Shiraz University, Shiraz (Iran, Islamic Republic of); Poursasan, Najmeh; Moosavi-Movahedi, Ali-Akbar [Institute of Biochemistry and Biophysics (IBB), the University of Tehran, Tehran (Iran, Islamic Republic of)

    2015-03-15

    This study describes HSA binding properties of two cyclometalated platinum (II) complexes with non-leaving lipophilic ligands; deprotonated 2-phenylpyridine (ppy): C{sub 1} and deprotonated benzo [h]quinolone (bhq): C{sub 2}, using UV–vis, fluorescence and circular dichroism (CD) spectroscopy. The absorption spectra of HSA decreased in the presence of increasing concentration of these complexes, reflecting HSA structural alteration after drug's binding. Also the thermodynamic parameters (ΔG, ΔH and ΔS) that obtained from Trp fluorescence study revealed that the interaction between these complexes and HSA were spontaneous. In addition, C{sub 1} with flexible chemical structure indicated significantly higher fluorescence quenching and binding affinity to HSA than C{sub 2} which possesses a higher structural rigidity. The ANS fluorescence results also indicated that two Pt (II) complexes were competing for binding to the hydrophobic regions of HSA. Moreover, CD results demonstrated that C{sub 2} complex induced alteration of HSA conformation to more significant extent compared to C{sub 1}. The molecular docking results revealed the involvement of π–π stacking and hydrophobic interaction between these complexes and the protein. Overall, this study may highlight the significance of structural flexibility in designing of future anticancer Pt (II) complexes with improved binding affinity for HSA. - Highlights: • HSA is a general transport carrier for a wide variety of ligands such as metabolites and pharmaceutical drugs. • The HSA binding properties of two structurally related cyclometallated platinum (II) complexes (C{sub 1} and C{sub 2}) were studied. • The complexes can bind to HSA and induce structural alteration in this protein. • The thermodynamic parameters revealed that the interactions were spontaneous and mainly hydrophobic driven. • C{sub 1} with flexible chemical structure indicated a higher binding affinity for HSA than C{sub 2}.

  5. Study of the interaction between two newly synthesized cyclometallated platinum (II) complexes and human serum albumin: Spectroscopic characterization and docking simulation

    International Nuclear Information System (INIS)

    This study describes HSA binding properties of two cyclometalated platinum (II) complexes with non-leaving lipophilic ligands; deprotonated 2-phenylpyridine (ppy): C1 and deprotonated benzo [h]quinolone (bhq): C2, using UV–vis, fluorescence and circular dichroism (CD) spectroscopy. The absorption spectra of HSA decreased in the presence of increasing concentration of these complexes, reflecting HSA structural alteration after drug's binding. Also the thermodynamic parameters (ΔG, ΔH and ΔS) that obtained from Trp fluorescence study revealed that the interaction between these complexes and HSA were spontaneous. In addition, C1 with flexible chemical structure indicated significantly higher fluorescence quenching and binding affinity to HSA than C2 which possesses a higher structural rigidity. The ANS fluorescence results also indicated that two Pt (II) complexes were competing for binding to the hydrophobic regions of HSA. Moreover, CD results demonstrated that C2 complex induced alteration of HSA conformation to more significant extent compared to C1. The molecular docking results revealed the involvement of π–π stacking and hydrophobic interaction between these complexes and the protein. Overall, this study may highlight the significance of structural flexibility in designing of future anticancer Pt (II) complexes with improved binding affinity for HSA. - Highlights: • HSA is a general transport carrier for a wide variety of ligands such as metabolites and pharmaceutical drugs. • The HSA binding properties of two structurally related cyclometallated platinum (II) complexes (C1 and C2) were studied. • The complexes can bind to HSA and induce structural alteration in this protein. • The thermodynamic parameters revealed that the interactions were spontaneous and mainly hydrophobic driven. • C1 with flexible chemical structure indicated a higher binding affinity for HSA than C2

  6. Synthesis, characterization, molecular docking and DNA binding studies of Al(III), Ga(III) and In(III) water-soluble complexes

    Science.gov (United States)

    Shorkaei, Mohammad Ranjkesh; Asadi, Zahra; Asadi, Mozaffar

    2016-04-01

    In this work three new water-soluble aluminum(III), gallium(III) and indium(III) Schiff base complexes; Na2[M(L)NO3]; where L denotes; N,N'-bis(5-sulfosalicyliden)-1,2-phenylendiamin (salsophen) were synthesized and characterized by UV-vis, 1HNMR, FT-IR spectroscopy, thermal gravimetry (TG) and elemental analysis. To study the biological preference with the molecular target DNA, interaction of these complexes with DNA have been explored by employing various biophysical methods including absorption spectra, fluorescence spectra, cyclic voltammetry and viscosity measurement. The Kb values at 298 K were found to be 1.17 × 104 for Al(III), 1.35 × 104 for Ga(III) and 1.64 × 104 M-1 for In(III) complexes, respectively. These results suggesting the greater binding propensity of In(III) complexes. Additionally molecular docking was carried out to ascertain the mode of action towards the molecular target DNA.

  7. Synthesis, interactions, molecular structure, biological properties and molecular docking studies on Mn, Co, Zn complexes containing acetylacetone and pyridine ligands with DNA duplex.

    Science.gov (United States)

    Thamilarasan, V; Sengottuvelan, N; Stalin, N; Srinivasan, P; Chakkaravarthi, G

    2016-07-01

    Three metal complexes (1-3) of the type [Mn(acac)2(py)·H2O] (1), [Co(acac)2(py)·H2O] (2) and [Zn(acac)2(py)·H2O] (3), [Where acac=acetylacetone, py=pyridine] were synthesized and characterized by spectral (UV-vis, FT-IR, ESI-mass) analysis. The structure of complex 2 has been determined by single crystal X-ray diffraction studies and the configuration of ligand-coordinated to metal(II) ion was well described as distorted octahedral coordination geometry. The interaction of the complexes with CT-DNA has been explored by absorption, fluorescence, circular dichromism spectroscopy, viscosity measurements and molecular docking studies. The intrinsic binding constant Kb of complexes 1-3 with CT-DNA obtained from UV-vis absorption spectral studies were 2.1×10(4), 2.1×10(5) and 1.98×10(4)M(-1), respectively, which revealed that the complexes could interact with CT-DNA through groove binding. The results indicated that the complexes (1-3) were able to bind to DNA with different binding affinity, in the order: 2>1>3. The interaction of the compounds with bovine serum albumins were also investigated using fluorescence methods and the gel electrophoresis assay demonstrates weak cleavage ability of the pBR322 plasmid DNA in the presence of the metal complexes (1-3) with various activators. Further, the in vitro cytotoxic effect of the complexes were examined on cancerous cell line, with human breast cancer cells MCF-7. PMID:27104666

  8. Energetic Mechanism of Cytochrome c-Cytochrome c Oxidase Electron Transfer Complex Formation under Turnover Conditions Revealed by Mutational Effects and Docking Simulation.

    Science.gov (United States)

    Sato, Wataru; Hitaoka, Seiji; Inoue, Kaoru; Imai, Mizue; Saio, Tomohide; Uchida, Takeshi; Shinzawa-Itoh, Kyoko; Yoshikawa, Shinya; Yoshizawa, Kazunari; Ishimori, Koichiro

    2016-07-15

    Based on the mutational effects on the steady-state kinetics of the electron transfer reaction and our NMR analysis of the interaction site (Sakamoto, K., Kamiya, M., Imai, M., Shinzawa-Itoh, K., Uchida, T., Kawano, K., Yoshikawa, S., and Ishimori, K. (2011) Proc. Natl. Acad. Sci. U.S.A. 108, 12271-12276), we determined the structure of the electron transfer complex between cytochrome c (Cyt c) and cytochrome c oxidase (CcO) under turnover conditions and energetically characterized the interactions essential for complex formation. The complex structures predicted by the protein docking simulation were computationally selected and validated by the experimental kinetic data for mutant Cyt c in the electron transfer reaction to CcO. The interaction analysis using the selected Cyt c-CcO complex structure revealed the electrostatic and hydrophobic contributions of each amino acid residue to the free energy required for complex formation. Several charged residues showed large unfavorable (desolvation) electrostatic interactions that were almost cancelled out by large favorable (Columbic) electrostatic interactions but resulted in the destabilization of the complex. The residual destabilizing free energy is compensated by the van der Waals interactions mediated by hydrophobic amino acid residues to give the stabilized complex. Thus, hydrophobic interactions are the primary factors that promote complex formation between Cyt c and CcO under turnover conditions, whereas the change in the electrostatic destabilization free energy provides the variance of the binding free energy in the mutants. The distribution of favorable and unfavorable electrostatic interactions in the interaction site determines the orientation of the binding of Cyt c on CcO. PMID:27226541

  9. CT-docking patient stretcher

    International Nuclear Information System (INIS)

    This paper assesses the use of a patient stretcher that directly docks to a CT scanner for acutely injured and/or critically ill patients. The stretcher permits performance of radiography and acts as a platform for critical care monitoring and patient support devices. During a 1-year period, the prototype CT-docking stretcher was used for 35 patients sustaining acute trauma and 25 patients from critical care units. Observations were elicited from physicians, nurses and technologists concerning the advantages or disadvantages of the docking stretcher. Advantages of the CT-docking stretcher included time saved in moving patients to the CT table from the admitting/emergency ward, transfer of critically ill patients onto the stretcher in the controlled environment of the intensive care unit rather than the CT suite, increasing CT throughput by direct docking of the patient stretcher to the CT scanner rather than manual transfer of complex support and monitoring devices with the patient, decreased risk associated with physical movement of patients with potentially unstable spinal injuries or unstable physiologic status, and decrease in potential for injury to medical personnel performing patient transfer

  10. Synthesis, characterization, antiproliferative and molecular docking study of new half sandwich Ir(III), Rh(III) and Ru(II) complexes.

    Science.gov (United States)

    Thangavel, Saravanan; Paulpandi, Manickam; Friedrich, Holger B; Murugan, Kadarkarai; Kalva, Sukesh; Skelton, Adam A

    2016-06-01

    The new carbazole N,N' ligand containing [(η(5)-C5Me5)MCl(L)]PF6, (M=Ir (1) and Rh (2)) and [(η(6)-C6H6)RuCl(L)]PF6 (3) (C5Me5=pentamethylcyclopentadienyl, L=9-ethyl-N-(pyridine-2-yl methylene)-9H-carbazole-3-amine) complexes has been synthesized and characterized by (1)H NMR, (13)C NMR, 2D NMR, melting point analysis, electronic absorption, infrared spectroscopy, HR-Mass spectroscopy and elemental analyses. The crystal structure of the [(η(5)-C5Me5)RhCl(L)]PF6 has been confirmed by single crystal XRD. The anticancer study of the synthesized complexes 1-3 clearly showed a potent inhibitor of human breast cancer cells (MCF-7) under in vitro conditions. The inhibitory concentrations (IC50) of the complexes 1-3 were determined at low (5, 6 and 8μM) concentration against the MCF-7 human breast cancer cell line. Further cytotoxic, cell cycle and nuclear studies confirmed that the novel half sandwich Ir(III), Rh(III) and Ru(II) complexes could be effective against MCF-7 human breast cancer cell proliferation. Moreover the results indicate that anticancer in vitro activity of complexes 1-3 falls in the order of 1>2>3. A molecular docking study of the complexes 1-3 showed the nature of binding energy, H-bond and hydrophobic interactions with the cyclooxygenase-2 (COX-2) receptor. PMID:26918899

  11. Synthesis, spectroscopic properties, molecular docking, anti-colon cancer and anti-microbial studies of some novel metal complexes for 2-amino-4-phenylthiazole derivative

    Science.gov (United States)

    Al-Harbi, Sami A.; Bashandy, Mahmoud S.; Al-Saidi, Hammed M.; Emara, Adel A. A.; Mousa, Tarek A. A.

    2015-06-01

    This article describes the synthesis of novel bidentate Schiff base (H2L) from condensation of 2-amino-4-phenylthiazole (APT) with 4,6-diacetylresorcinol (DAR) in the molar ratio 2:1. We studied interaction of ligand (H2L) with transition metal ions such as Cr(III), Fe(III), Cu(II), Zn(II) and Cd(II). The ligand (H2L) has two bidentate sets of (N-O) units which can coordinate with two metal ions to afford novel binuclear metal complexes. The directions of coordinate bonds are from nitrogen atoms of azomethine groups and oxygen atoms of the phenolic groups. Structures of the newly synthesized complexes were confirmed by elemental analysis, IR, UV, 1H NMR, ESR, TGA and mass spectral data. All of the newly synthesized complexes were evaluated for their antibacterial and anti-fungal activities. They were also evaluated for their in vitro anticancer activity against human colon carcinoma cells (HCT-116) and mammalian cells of African green monkey kidney (VERO). The Cu(II) complex with selectivity index (S.I.) = 21.26 exhibited better activity than methotrexate (MTX) as a reference drug with S.I. value = 13.30, while Zn(II) complex with S.I. value = 10.24 was found to be nearly as active as MTX. Molecular docking studies further helped in understanding the mode of action of the compounds through their various interactions with active sites of dihydrofolate reductase (DHFR) enzyme. The observed activity of Fe(III) and Cu(II) complexes gave rise to the conclusion that they might exert their action through inhibition of the DHFR enzyme.

  12. miR-124-regulated RhoG reduces neuronal process complexity via ELMO/Dock180/Rac1 and Cdc42 signalling

    Science.gov (United States)

    Franke, Kristin; Otto, Wolfgang; Johannes, Sascha; Baumgart, Jan; Nitsch, Robert; Schumacher, Stefan

    2012-01-01

    The small GTPase RhoG plays a central role in actin remodelling during diverse biological processes such as neurite outgrowth, cell migration, phagocytosis of apoptotic cells, and the invasion of pathogenic bacteria. Although it is known that RhoG stimulates neurite outgrowth in the rat pheochromocytoma PC12 cell line, neither the physiological function nor the regulation of this GTPase in neuronal differentiation is clear. Here, we identify RhoG as an inhibitor of neuronal process complexity, which is regulated by the microRNA miR-124. We find that RhoG inhibits dendritic branching in hippocampal neurons in vitro and in vivo. RhoG also inhibits axonal branching, acting via an ELMO/Dock180/Rac1 signalling pathway. However, RhoG inhibits dendritic branching dependent on the small GTPase Cdc42. Finally, we show that the expression of RhoG in neurons is suppressed by the CNS-specific microRNA miR-124 and connect the regulation of RhoG expression by miR-124 to the stimulation of neuronal process complexity. Thus, RhoG emerges as a cellular conductor of Rac1 and Cdc42 activity, in turn regulated by miR-124 to control axonal and dendritic branching. PMID:22588079

  13. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene

    2003-01-01

    search spaces effectively and is one of the commonly used methods for flexible ligand docking. During the last decade, several EAs using different variation operators have been introduced, such as the ones provided with the AutoDock program. In this paper we evaluate the performance of different EA......The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...... settings such as choice of variation operators, population size, and usage of local search. The comparison is performed on a suite of six docking problems previously used to evaluate the performance of search algorithms provided with the AutoDock program package. The results from our investigation confirm...

  14. DIRECT SHIPMENT VS. CROSS DOCKING

    OpenAIRE

    TAMÁS BÁNYAI

    2012-01-01

    The globalization of production and service enterprises increased the complexity of supply chain systems and processes. The complexity of supply problems leaded to the development of new shipment strategies. The optimal design of supply chain is an important success factor of the economical operation of enterprises. Within the frame of this paper the author compare the costs of the direct shipment and the cross docking supply from the point of view of all members of supply chain. Cross dockin...

  15. Synthesis, structure, DFT calculations, electrochemistry, fluorescence, DNA binding and molecular docking aspects of a novel oxime based ligand and its palladium(II) complex.

    Science.gov (United States)

    Bandyopadhyay, Nirmalya; Pradhan, Ankur Bikash; Das, Suman; Lu, Liping; Zhu, Miaoli; Chowdhury, Shubhamoy; Naskar, Jnan Prakash

    2016-07-01

    A novel oxime based ligand, phenyl-(pyridine-2-yl-hydrazono)-acetaldehyde oxime (LH), and its palladium(II) complex (1) have been synthesised and spectroscopically characterised. The ligand crystallizes in the monoclinic space group (P21/c). The X-ray crystal structure of the ligand shows that it forms a hydrogen bonded helical network. The ligand has been characterised by C, H and N microanalyses, (1)H and (13)C NMR, ESI-MS, FT-IR and UV-Vis spectral measurements. Geometry optimizations at the level of DFT show that the Pd(II) centre is nested in a square-planar 'N3Cl' coordination chromophore. The diamagnetic palladium complex has been characterised by C, H and N microanalyses, FAB-MS, FT-IR, UV-Vis spectra and molar electrical conductivity measurements. The observed electronic spectrum of 1 correlates with our theoretical findings as evaluated through TD-DFT. 1 displays quasi-reversible Pd(II)/Pd(III) and Pd(III)/Pd(IV) redox couples in its CV in acetonitrile. 1 is nine-fold more emissive with respect to the binding ligand. Biophysical studies have been carried out to show the DNA binding aspects of both the ligand and complex. The binding constants for the ligand and complex were found to be 3.93×10(4) and 1.38×10(3)M(-1) respectively. To have an insight into the mode of binding of LH and 1 with CT DNA a hydrodynamic study was also undertaken. The mode of binding has also been substantiated through molecular docking. A promising groove binding efficacy has been revealed for the ligand. PMID:27179300

  16. Protein-protein docking with F(2Dock 2.0 and GB-rerank.

    Directory of Open Access Journals (Sweden)

    Rezaul Chowdhury

    Full Text Available MOTIVATION: Computational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F(2 Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowledge-based interface propensity term with FFT formulation, a set of novel knowledge-based filters and finally a solvation energy (GBSA based reranking technique. Our algorithms are based on highly efficient data structures including the dynamic packing grids and octrees which significantly speed up the computations and also provide guaranteed bounds on approximation error. RESULTS: The improved affinity functions show superior performance compared to their traditional counterparts in finding correct docking poses at higher ranks. We found that the new filters and the GBSA based reranking individually and in combination significantly improve the accuracy of docking predictions with only minor increase in computation time. We compared F(2 Dock 2.0 with ZDock 3.0.2 and found improvements over it, specifically among 176 complexes in ZLab Benchmark 4.0, F(2 Dock 2.0 finds a near-native solution as the top prediction for 22 complexes; where ZDock 3.0.2 does so for 13 complexes. F(2 Dock 2.0 finds a near-native solution within the top 1000 predictions for 106 complexes as opposed to 104 complexes for ZDock 3.0.2. However, there are 17 and 15 complexes where F(2 Dock 2.0 finds a solution but ZDock 3.0.2 does not and vice versa; which indicates that the two docking protocols can also complement each other. AVAILABILITY: The docking protocol has been implemented as a server with a graphical client (TexMol which allows the user to manage multiple docking jobs, and visualize the docked poses and interfaces. Both the server and client are available for download. Server

  17. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

    Science.gov (United States)

    Ravindranath, Pradeep Anand; Forli, Stefano; Goodsell, David S; Olson, Arthur J; Sanner, Michel F

    2015-12-01

    Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; and 2) increased number of false positives, calling for scoring functions tailored for flexible receptor docking. We present AutoDockFR-AutoDock for Flexible Receptors (ADFR), a new docking engine based on the AutoDock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm (GA) and customized scoring function. We validate ADFR using the Astex Diverse Set, demonstrating an increase in efficiency and reliability of its GA over the one implemented in AutoDock4. We demonstrate greatly increased success rates when cross-docking ligands into apo receptors that require side-chain conformational changes for ligand binding. These cross-docking experiments are based on two datasets: 1) SEQ17 -a receptor diversity set containing 17 pairs of apo-holo structures; and 2) CDK2 -a ligand diversity set composed of one CDK2 apo structure and 52 known bound inhibitors. We show that, when cross-docking ligands into the apo conformation of the receptors with up to 14 flexible side-chains, ADFR reports more correctly cross-docked ligands than AutoDock Vina on both datasets with solutions found for 70.6% vs. 35.3% systems on SEQ17, and 76.9% vs. 61.5% on CDK2. ADFR also outperforms AutoDock Vina in number of top ranking solutions on both datasets. Furthermore, we show that correctly docked CDK2 complexes re-create on average 79.8% of all pairwise atomic interactions between the ligand and moving receptor atoms in the holo complexes. Finally, we show that down

  18. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

    Directory of Open Access Journals (Sweden)

    Pradeep Anand Ravindranath

    2015-12-01

    Full Text Available Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1 exponential growth of the search space, demanding more efficient search methods; and 2 increased number of false positives, calling for scoring functions tailored for flexible receptor docking. We present AutoDockFR-AutoDock for Flexible Receptors (ADFR, a new docking engine based on the AutoDock4 scoring function, which addresses the aforementioned challenges with a new Genetic Algorithm (GA and customized scoring function. We validate ADFR using the Astex Diverse Set, demonstrating an increase in efficiency and reliability of its GA over the one implemented in AutoDock4. We demonstrate greatly increased success rates when cross-docking ligands into apo receptors that require side-chain conformational changes for ligand binding. These cross-docking experiments are based on two datasets: 1 SEQ17 -a receptor diversity set containing 17 pairs of apo-holo structures; and 2 CDK2 -a ligand diversity set composed of one CDK2 apo structure and 52 known bound inhibitors. We show that, when cross-docking ligands into the apo conformation of the receptors with up to 14 flexible side-chains, ADFR reports more correctly cross-docked ligands than AutoDock Vina on both datasets with solutions found for 70.6% vs. 35.3% systems on SEQ17, and 76.9% vs. 61.5% on CDK2. ADFR also outperforms AutoDock Vina in number of top ranking solutions on both datasets. Furthermore, we show that correctly docked CDK2 complexes re-create on average 79.8% of all pairwise atomic interactions between the ligand and moving receptor atoms in the holo complexes. Finally, we

  19. Electrostatics in protein–protein docking

    OpenAIRE

    Heifetz, Alexander; Katchalski-Katzir, Ephraim; Eisenstein, Miriam

    2002-01-01

    A novel geometric-electrostatic docking algorithm is presented, which tests and quantifies the electrostatic complementarity of the molecular surfaces together with the shape complementarity. We represent each molecule to be docked as a grid of complex numbers, storing information regarding the shape of the molecule in the real part and information regarding the electrostatic character of the molecule in the imaginary part. The electrostatic descriptors are derived from the electrostatic pote...

  20. Highly flexible protein-peptide docking using CABS-dock

    OpenAIRE

    Ciemny, Maciej Pawel; Kurcinski, Mateusz; Kozak, Konrad Jakub; Kolinski, Andrzej; Kmiecik, Sebastian

    2016-01-01

    Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and bi...

  1. VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy.

    Directory of Open Access Journals (Sweden)

    Joan Segura

    Full Text Available The experimental determination of the structure of protein complexes cannot keep pace with the generation of interactomic data, hence resulting in an ever-expanding gap. As the structural details of protein complexes are central to a full understanding of the function and dynamics of the cell machinery, alternative strategies are needed to circumvent the bottleneck in structure determination. Computational protein docking is a valid and valuable approach to model the structure of protein complexes. In this work, we describe a novel computational strategy to predict the structure of protein complexes based on data-driven docking: VORFFIP-driven dock (V-D2OCK. This new approach makes use of our newly described method to predict functional sites in protein structures, VORFFIP, to define the region to be sampled during docking and structural clustering to reduce the number of models to be examined by users. V-D2OCK has been benchmarked using a validated and diverse set of protein complexes and compared to a state-of-art docking method. The speed and accuracy compared to contemporary tools justifies the potential use of VD2OCK for high-throughput, genome-wide, protein docking. Finally, we have developed a web interface that allows users to browser and visualize V-D2OCK predictions from the convenience of their web-browsers.

  2. Extracellular Signal-Regulated Kinase 2 (ERK2) Phosphorylation Sites and Docking Domain on the Nuclear Pore Complex Protein Tpr Cooperatively Regulate ERK2-Tpr Interaction

    Czech Academy of Sciences Publication Activity Database

    Vomastek, Tomáš; Iwanicky, M. P.; Burack, W. R.; Tiwari, D.; Kumar, D.; Parsons, J. T.; Weber, M. J.; Nandicoori, V. K.

    2008-01-01

    Roč. 28, č. 22 (2008), s. 6954-6966. ISSN 0270-7306 R&D Projects: GA AV ČR IAA500200716 Institutional research plan: CEZ:AV0Z50200510 Keywords : erk * docking domain * cell growth Subject RIV: EE - Microbiology, Virology Impact factor: 5.942, year: 2008

  3. NMR-based docking of protein-protein complexes : the human UbcH5b-CNOT4 ubiquitination complex

    NARCIS (Netherlands)

    Dominguez, Cyril

    2004-01-01

    Understanding the molecular and functional interactions among macromolecular complexes, as well as their changes associated with time, cell type or disease state will be invaluable for human health, and will have direct implications, for example, in pharmaceutical research to identify and select pot

  4. Flexible protein-peptide docking using CABS-dock with knowledge about the binding site

    OpenAIRE

    Kurcinski, Mateusz; Ciemny, Maciej Pawel; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

    2016-01-01

    Despite considerable efforts, structural prediction of protein-peptide complexes is still a very challenging task, mainly due to two reasons: high flexibility of the peptides and transient character of their interactions with proteins. Recently we have developed an automated web server CABS-dock (http://biocomp.chem.uw.edu.pl/CABSdock), which conducts flexible protein-peptide docking without any knowledge about the binding site. Our method allows for full flexibility of the peptide, whereas t...

  5. Arbitrary protein−protein docking targets biologically relevant interfaces

    OpenAIRE

    Martin Juliette; Lavery Richard

    2012-01-01

    Abstract Background Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible ...

  6. EFFECTS OF RESISTANCE EXERCISES AND COMPLEX DECONGESTIVE THERAPY ON ARM FUNCTION AND MUSCULAR STRENGTH IN BREAST CANCER RELATED LYMPHEDEMA.

    Science.gov (United States)

    Do, J H; Kim, W; Cho, Y K; Lee, J; Song, E J; Chun, Y M; Jeon, J Y

    2015-12-01

    The incorporation of resistance exercises into the lifestyle of patients with lymphedema is understudied and an emerging interest. We investigated the effectiveness and results of adding a moderate intensity resistance exercise program for 8 weeks in conjunction with intensive CDT for 1 or 2 weeks (depending on severity) on arm volume, arm function, QOL, and muscular strength in patients with breast cancer-related lymphedema. This prospective, pilot trial included forty-four patients with a history of breast cancer who were beginning complex decongestive therapy for lymphedema. They were assigned to either the intervention (n = 22) or control (n = 22). groups. The intervention comprised of resis- tance band exercises 5 times a week for 8 weeks. These were initially supervised during the intensive lymphedema treatment, but performed independently during the study period. Limb volume, muscular strength, and the European Organization for Research and Treatment of Cancer QOL Questionnaire C30 (EORTC QLQ-C30), EORTC-Breast Cancer-Specific QOL Questionnaire (EORTC QLQ-BR23), and Disabilities of Arm, Shoulder, and Hand (DASH) questionnaires were assessed at baseline and at 8 weeks. After 8 weeks, the intervention group demonstrated statistically significant differences (p cancer related lymphedema during and shortly post intensive CDT lymphedema treatment. PMID:27164764

  7.  α-Cyclodextrin dimer complexes of dopamine and levodopa derivatives to assess drug delivery to the central nervous system: ADME and molecular docking studies

    OpenAIRE

    Shityakov S; Broscheit J; Förster C

    2012-01-01

    Sergey Shityakov, Jens Broscheit, Carola FörsterDepartment of Anesthesiology and Critical Care, University of Würzburg, Würzburg, GermanyAbstract: This paper attempts to predict and emphasize molecular interactions of dopamine, levodopa, and their derivatives (Dopimid compounds) containing 2-phenyl-imidazopyridine moiety with the α-cyclodextrin dimer in order to assess and improve drug delivery to the central nervous system. The molecular docking method is...

  8. α-Cyclodextrin dimer complexes of dopamine and levodopa derivatives to assess drug delivery to the central nervous system: ADME and molecular docking studies

    OpenAIRE

    Shityakov, Sergey

    2012-01-01

    Sergey Shityakov, Jens Broscheit, Carola FörsterDepartment of Anesthesiology and Critical Care, University of Würzburg, Würzburg, GermanyAbstract: This paper attempts to predict and emphasize molecular interactions of dopamine, levodopa, and their derivatives (Dopimid compounds) containing 2-phenyl-imidazopyridine moiety with the α-cyclodextrin dimer in order to assess and improve drug delivery to the central nervous system. The molecular docking method is...

  9. The Canadian Armed Forces “YouTube War”: A Cross-Border Military-Social Media Complex

    OpenAIRE

    Tanner Mirrlees

    2015-01-01

    The goal of this paper is to conceptualize, contextualize, and critically analyze the Canadian Armed Forces’ (CAF) use of YouTube to promote itself, recruit soldiers, and frame its role in the post-9/11 U.S.-led NATO war in Afghanistan. The first section of this paper engages with scholarship on war and the media, the military-industrial-communications complex (MICC), and YouTube War to conceptualize YouTube as a tool and contested battle-space of 21st century new media wars. The second secti...

  10. Endeavor Approaches Docking Port of ISS

    Science.gov (United States)

    2002-01-01

    Pictured here is the forward docking port on the International Space Station's (ISS) Destiny Laboratory as seen by one of the STS-111 crewmembers from the Space Shuttle Orbiter Endeavour just prior to docking. In June 2002, STS-111 provided the Space Station with a new crew, Expedition Five, replacing Expedition Four after remaining a record-setting 196 days in space. Three spacewalks enabled the STS-111 crew to accomplish additional mission objectives: the delivery and installation of a new platform for the ISS robotic arm, the Mobile Base System (MBS) which is an important part of the Station's Mobile Servicing System allowing the robotic arm to travel the length of the Station; the replacement of a wrist roll joint on the Station's robotic arm; and unloading supplies and science experiments form the Leonardo Multi-Purpose Logistics Module, which made its third trip to the orbital outpost. The STS-111 mission, the 14th Shuttle mission to visit the ISS, was launched on June 5, 2002 and landed June 19, 2002.

  11. A protein–DNA docking benchmark

    NARCIS (Netherlands)

    van Dijk, M.; Bonvin, A.M.J.J.

    2008-01-01

    We present a protein–DNA docking benchmark containing 47 unbound–unbound test cases of which 13 are classified as easy, 22 as intermediate and 12 as difficult cases. The latter shows considerable structural rearrangement upon complex formation. DNA-specific modifications such as flipped out bases an

  12. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

    OpenAIRE

    Jain, Ajay N.

    2009-01-01

    Computational methods for docking ligands have been shown to be remarkably dependent on precise protein conformation, where acceptable results in pose prediction have been generally possible only in the artificial case of re-docking a ligand into a protein binding site whose conformation was determined in the presence of the same ligand (the “cognate” docking problem). In such cases, on well curated protein/ligand complexes, accurate dockings can be returned as top-scoring over 75% of the tim...

  13. A three-arm current comparator bridge, for impedance comparisons over the complex plane

    CERN Document Server

    Callegaro, Luca; Ortolano, Massimo; Pourdanesh, Faranak

    2014-01-01

    We present here the concept of three-arm current comparator impedance bridge, which allows comparisons among three unlike impedances. Its purpose is the calibration of impedances having arbitrary phase angles, against calibrated nearly-pure impedances. An analysis of the bridge optimal setting and proper operation is presented. To test the concept, a two terminal-pair digitally-assisted bridge has been realized; measurements of an air-core inductor and of an RC network versus decade resistance and capacitance standards, at kHz frequency, have been performed. The bridge measurements are compatible with previous knowledge of the standards' values with relative deviations in the 10^-5 -- 10^-6 range.

  14. Ruthenium(II) pincer complexes with oxazoline arms for efficient transfer hydrogenation reactions

    KAUST Repository

    Chen, Tao

    2012-08-01

    Well-defined P NN CN pincer ruthenium complexes bearing both strong phosphine and weak oxazoline donors were developed. These easily accessible complexes exhibit significantly better catalytic activity in transfer hydrogenation of ketones compared to their PN 3P analogs. These reactions proceed under mild and base-free conditions via protonation- deprotonation of the \\'NH\\' group in the aromatization-dearomatization process. © 2012 Elsevier Ltd. All rights reserved.

  15. Spacecraft rendezvous and docking

    DEFF Research Database (Denmark)

    Jørgensen, John Leif

    1999-01-01

    been based entirely on direct human supervision and control. This paper describes a vision-based system and methodology, that autonomously generates accurate guidance information that may assist a human operator in performing the tasks associated with both the rendezvous and docking navigation...... procedures. The method described generates, based on a single camera and a priory information about the target vehicle and orbit data, all necessary guidance information for closed-loop autonomous navigation, from first detection at far distance, to a close up a hold point. Furthermore, the system provide......The phenomenons and problems encountered when a rendezvous manoeuvre, and possible docking, of two spacecrafts has to be performed, have been the topic for numerous studies, and, details of a variety of scenarios has been analysed. So far, all solutions that has been brought into realization has...

  16. Essential role of Elmo1 in Dock2-dependent lymphocyte migration.

    Science.gov (United States)

    Stevenson, Catherine; de la Rosa, Gonzalo; Anderson, Christopher S; Murphy, Patrick S; Capece, Tara; Kim, Minsoo; Elliott, Michael R

    2014-06-15

    Elmo1 and Elmo2 are highly homologous cytoplasmic adaptor proteins that interact with Dock family guanine nucleotide exchange factors to promote activation of the small GTPase Rac. In T lymphocytes, Dock2 is essential for CCR7- and CXCR4-dependent Rac activation and chemotaxis, but the role of Elmo proteins in regulating Dock2 function in primary T cells is not known. In this article, we show that endogenous Elmo1, but not Elmo2, interacts constitutively with Dock2 in mouse and human primary T cells. CD4(+) T cells from Elmo1(-/-) mice were profoundly impaired in polarization, Rac activation, and chemotaxis in response to CCR7 and CXCR4 stimulation. Transfection of full-length Elmo1, but not Elmo2 or a Dock2-binding mutant of Elmo1, rescued defective migration of Elmo1(-/-) T cells. Interestingly, Dock2 protein levels were reduced by 4-fold in Elmo1(-/-) lymphocytes despite normal levels of Dock2 mRNA. Dock2 polyubiquitination was increased in Elmo1(-/-) T cells, and treatment with proteasome inhibitors partially restored Dock2 levels in Elmo1(-/-) T cells. Finally, we show that Dock2 is directly ubiquitinated in CD4(+) T cells and that Elmo1 expression in heterologous cells inhibits ubiquitination of Dock2. Taken together, these findings reveal a previously unknown, nonredundant role for Elmo1 in controlling Dock2 levels and Dock2-dependent T cell migration in primary lymphocytes. Inhibition of Dock2 has therapeutic potential as a means to control recruitment of pathogenic lymphocytes in diseased tissues. This work provides valuable insights into the molecular regulation of Dock2 by Elmo1 that can be used to design improved inhibitors that target the Elmo-Dock-Rac signaling complex. PMID:24821968

  17. Vision-guided heterogeneous mobile robot docking

    Science.gov (United States)

    Spofford, John R.; Blitch, John; Klarquist, William N.; Murphy, Robin R.

    1999-08-01

    Teams of heterogeneous mobile robots are a key aspect of future unmanned system for operations in complex and dynamic urban environments, such as that envisioned by DARPA's Tactical Mobile Robotics program. One examples of an interaction among such team members is the docking of small robot of limited sensory and processing capability with a larger, more capable robot. Applications for such docking include the transfer of power, data, and materia, as well as physically combined maneuver or manipulation. A two-robot system is considered in this paper. The smaller 'throwable' robot contains a video camera capable of imaging the larger 'packable' robot and transmitting the imagery. The packable robot can both sense the throwable robot through an onboard camera, as well as sense itself through the throwable robot's transmitted video, and is capable of processing imagery from either source. This paper describes recent results in the development of control and sensing strategies for automatic mid-range docking of these two robots. Decisions addressed include the selection of which robot's image sensor to use and which robot to maneuver. Initial experimental results are presented for docking using sensor data from each robot.

  18. Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: impact on GOLD docking performance.

    Science.gov (United States)

    Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine

    2012-05-25

    GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach. PMID:22462609

  19. Investigation of MM-PBSA rescoring of docking poses.

    Science.gov (United States)

    Thompson, David C; Humblet, Christine; Joseph-McCarthy, Diane

    2008-05-01

    Target-based virtual screening is increasingly used to generate leads for targets for which high quality three-dimensional (3D) structures are available. To allow large molecular databases to be screened rapidly, a tiered scoring scheme is often employed whereby a simple scoring function is used as a fast filter of the entire database and a more rigorous and time-consuming scoring function is used to rescore the top hits to produce the final list of ranked compounds. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approaches are currently thought to be quite effective at incorporating implicit solvation into the estimation of ligand binding free energies. In this paper, the ability of a high-throughput MM-PBSA rescoring function to discriminate between correct and incorrect docking poses is investigated in detail. Various initial scoring functions are used to generate docked poses for a subset of the CCDC/Astex test set and to dock one set of actives/inactives from the DUD data set. The effectiveness of each of these initial scoring functions is discussed. Overall, the ability of the MM-PBSA rescoring function to (i) regenerate the set of X-ray complexes when docking the bound conformation of the ligand, (ii) regenerate the X-ray complexes when docking conformationally expanded databases for each ligand which include "conformation decoys" of the ligand, and (iii) enrich known actives in a virtual screen for the mineralocorticoid receptor in the presence of "ligand decoys" is assessed. While a pharmacophore-based molecular docking approach, PhDock, is used to carry out the docking, the results are expected to be general to use with any docking method. PMID:18465849

  20. Ruthenium-arene complexes of curcumin: X-ray and density functional theory structure, synthesis, and spectroscopic characterization, in vitro antitumor activity, and DNA docking studies of (p-cymene)Ru(curcuminato)chloro.

    Science.gov (United States)

    Caruso, Francesco; Rossi, Miriam; Benson, Aidan; Opazo, Cristian; Freedman, Daniel; Monti, Elena; Gariboldi, Marzia Bruna; Shaulky, Jodi; Marchetti, Fabio; Pettinari, Riccardo; Pettinari, Claudio

    2012-02-01

    The in vitro antiproliferative activity of the title compound on five tumor cell lines shows preference for the colon-rectal tumor HCT116, IC(50) = 13.98 μM, followed by breast MCF7 (19.58 μM) and ovarian A2780 (23.38 μM) cell lines; human glioblastoma U-87 and lung carcinoma A549 are less sensitive. A commercial curcumin reagent, also containing demethoxy and bis-demethoxy curcumin, was used to synthesize the title compound, and so (p-cymene)Ru(demethoxy-curcuminato)chloro was also isolated and chemically characterized. The crystal structure of the title compound shows (1) the chlorine atom linking two neighboring complexes through H-bonds with two O(hydroxyl), forming an infinite two-step network; (2) significant twist in the curcuminato, 20° between the planes of the two phenyl rings. This was also seen in the docking of the Ru-complex onto a rich guanine B-DNA decamer, where a Ru-N7(guanine) interaction is detected. This Ru-N7(guanine) interaction is also seen with ESI-MS on a Ru-complex-guanosine derivative. PMID:22204522

  1. Spacecraft rendezvous and docking

    DEFF Research Database (Denmark)

    Jørgensen, John Leif

    1999-01-01

    procedures. The method described generates, based on a single camera and a priory information about the target vehicle and orbit data, all necessary guidance information for closed-loop autonomous navigation, from first detection at far distance, to a close up a hold point. Furthermore, the system provide...... been based entirely on direct human supervision and control. This paper describes a vision-based system and methodology, that autonomously generates accurate guidance information that may assist a human operator in performing the tasks associated with both the rendezvous and docking navigation...

  2. A Holonic Logistics Execution System for Cross-docking (Een holonisch logistiek uitvoeringssysteem voor cross-docking)

    OpenAIRE

    Van Belle, Jan

    2013-01-01

    The coordination and control of cross-docking operations is a complex task and a challenging problem. A severe competition in the logistics sector and ever-increasing traffic (congestion) make that cross-docks should be able to operate efficiently in uncertain and dynamic environments. Moreover, the operational coordination and control is a going concern, so 'one-shot optimization' is not sufficient.As the logistics and manufacturing domain are characterized by similar properties (e.g. large ...

  3. Spectroscopic investigations of Eu3+-complexes with ligands containing multiple diglycolamide pendant arms in a room temperature ionic liquid

    International Nuclear Information System (INIS)

    Fluorescence spectroscopy was used to study the complexation of different ligands containing multiple diglycolamide (DGA) pendent arms such as T-DGA (tripodal diglycolamide), C4DGA (upper rim functionalized calix [4] arene with four DGA moieties), and C8DGA (both side functionalized calix [4] arene with eight DGA moieties) with Eu3+ in ionic liquids such as C4mimNTf2 and C8mimNTf2 (1-alkyl-3-methylimidazolium bis(trifluoromethylsulphonyl)imide). Mainly five sets of emission profiles were observed in all the spectra (1st set at∼580 nm assigned as the 5D0→7F0 transition, 2nd set at∼593 nm assigned as the 5D0→7F1 transition, 3rd set at∼613 nm assigned as the 5D0→7F2 transition, 4th set at∼650 nm assigned as the 5D0→7F3 transition, and 5th set at∼700 nm assigned as the 5D0→7F4 transition). The difference in the spectral features revealed that the nature of the complexes differs significantly from one another. Judd–Offelt constant Ω2, which is a measure of the covalency of the metal–ligand bond, follows the order Eu3+–C4DGA (C8mimNTf2)>Eu3+–C8DGA (C8mimNTf2)>Eu3+–TODGA (C4mimNTf2)>Eu3+–T-DGA (C4mimNTf2)>Eu3+aq. The high intensity of the 5D0→7F2 transitions in all complexes suggests that Eu3+ resides in a highly asymmetric environment. From the splitting patterns of the transitions, the local site symmetry around Eu3+ was found to be C2V for the Eu3+–T-DGA complex in both C4mimNTf2 and a 1:5 acetonitrile–water mixture, C4V for Eu3+–C8DGA and Eu3+–TODGA complexes, and either C1, C2, or CS for the Eu3+–C4DGA complex. A linear relationship between the 5D0–7F1 splitting vs E(5D0–7F0) and E(5D0–7F0) vs E(5D0–7F1) was observed. The crystal field parameters in the different complexes follow the trend Eu3+–C4DGA>Eu3+–TODGA>Eu3+–T-DGA in C4mimNTf2∼Eu3+–C8DGA>Eu3+–T-DGA in 5:1 acetonitrile-water mixture. - Highlights: • J–O parameters were obtained from luminescence data of Eu3+ –DGA complexes. • The studies

  4. Robotics in hostile environment I.S.I.S. robot - automatic positioning and docking with proximity and force feed back sensors

    International Nuclear Information System (INIS)

    Recent improvements in control command systems and the development of tactile proximity and force feed back sensors make it possible to robotize complex inspection and maintenance operations in hostile environment, which could have not been possible by classical remotely operated manipulators. We describe the I.S.I.S. robot characteristics, the control command system software principles and the tactile and force-torque sensors which have been developed for the different sequences of an hostile environment inspection and repair: access trajectories generation with obstacles shunning, final positioning and docking using parametric algorithms taking into account measurement of the end of arm proximity and force-torque sensors

  5. Cyclam Derivatives with a Bis(phosphinate) or a Phosphinato-Phosphonate Pendant Arm: Ligands for Fast and Efficient Copper(II) Complexation for Nuclear Medical Applications.

    Science.gov (United States)

    David, Tomáš; Kubíček, Vojtěch; Gutten, Ondrej; Lubal, Přemysl; Kotek, Jan; Pietzsch, Hans-Jürgen; Rulíšek, Lubomír; Hermann, Petr

    2015-12-21

    Cyclam derivatives bearing one geminal bis(phosphinic acid), -CH2PO2HCH2PO2H2 (H2L(1)), or phosphinic-phosphonic acid, -CH2PO2HCH2PO3H2 (H3L(2)), pendant arm were synthesized and studied as potential copper(II) chelators for nuclear medical applications. The ligands showed good selectivity for copper(II) over zinc(II) and nickel(II) ions (log KCuL = 25.8 and 27.7 for H2L(1) and H3L(2), respectively). Kinetic study revealed an unusual three-step complex formation mechanism. The initial equilibrium step leads to out-of-cage complexes with Cu(2+) bound by the phosphorus-containing pendant arm. These species quickly rearrange to an in-cage complex with cyclam conformation II, which isomerizes to another in-cage complex with cyclam conformation I. The first in-cage complex is quantitatively formed in seconds (pH ≈5, 25 °C, Cu:L = 1:1, cM ≈ 1 mM). At pH >12, I isomers undergo nitrogen atom inversion, leading to III isomers; the structure of the III-[Cu(HL(2))] complex in the solid state was confirmed by X-ray diffraction analysis. In an alkaline solution, interconversion of the I and III isomers is mutual, leading to the same equilibrium isomeric mixture; such behavior has been observed here for the first time for copper(II) complexes of cyclam derivatives. Quantum-chemical calculations showed small energetic differences between the isomeric complexes of H3L(2) compared with analogous data for isomeric complexes of cyclam derivatives with one or two methylphosphonic acid pendant arm(s). Acid-assisted dissociation proved the kinetic inertness of the complexes. Preliminary radiolabeling of H2L(1) and H3L(2) with (64)Cu was fast and efficient, even at room temperature, giving specific activities of around 70 GBq of (64)Cu per 1 μmol of the ligand (pH 6.2, 10 min, ca. 90 equiv of the ligand). These specific activities were much higher than those of H3nota and H4dota complexes prepared under identical conditions. The rare combination of simple ligand synthesis, very

  6. Focused grid-based resampling for protein docking and mapping.

    Science.gov (United States)

    Mamonov, Artem B; Moghadasi, Mohammad; Mirzaei, Hanieh; Zarbafian, Shahrooz; Grove, Laurie E; Bohnuud, Tanggis; Vakili, Pirooz; Ch Paschalidis, Ioannis; Vajda, Sandor; Kozakov, Dima

    2016-04-30

    The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein-protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near-native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands. © 2016 Wiley Periodicals, Inc. PMID:26837000

  7. Arbitrary protein−protein docking targets biologically relevant interfaces

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2012-05-01

    Full Text Available Abstract Background Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. Results In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking

  8. Arbitrary protein−protein docking targets biologically relevant interfaces

    International Nuclear Information System (INIS)

    Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking using PEBP (Phosphatidylethanolamine binding

  9. Technology Development of Automated Rendezvous and Docking/Capture Sensors and Docking Mechanism for the Asteroid Redirect Crewed Mission

    Science.gov (United States)

    Hinkel, Heather; Strube, Matthew; Zipay, John J.; Cryan, Scott

    2016-01-01

    This paper will describe the technology development efforts NASA has underway for Automated Rendezvous and Docking/Capture (AR&D/C) sensors and a docking mechanism and the challenges involved. The paper will additionally address how these technologies will be extended to other missions requiring AR&D/C whether robotic or manned. NASA needs AR&D/C sensors for both the robotic and crewed segments of the Asteroid Redirect Mission (ARM). NASA recently conducted a commonality assessment of the concept of operations for the robotic Asteroid Redirect Vehicle (ARV) and the crewed mission segment using the Orion spacecraft. The commonality assessment also considered several future exploration and science missions requiring an AR&D/C capability. Missions considered were asteroid sample return, satellite servicing, and planetary entry, descent, and landing. This assessment determined that a common sensor suite consisting of one or more visible wavelength cameras, a three-dimensional LIDAR along with long-wavelength infrared cameras for robustness and situational awareness could be used on each mission to eliminate the cost of multiple sensor developments and qualifications. By choosing sensor parameters at build-time instead of at design-time and, without having to requalify flight hardware, a specific mission can design overlapping bearing, range, relative attitude, and position measurement availability to suit their mission requirements with minimal non-recurring engineering costs. The resulting common sensor specification provides the union of all performance requirements for each mission and represents an improvement over the current systems used for AR&D/C today. These sensor specifications are tightly coupled to the docking system capabilities and requirements for final docking conditions. The paper will describe NASA's efforts to develop a standard docking system for use across NASA human spaceflight missions to multiple destinations. It will describe the current

  10. Optical Docking Aid Containing Fresnel Lenses

    Science.gov (United States)

    Pierce, Cole J.

    1995-01-01

    Proposed device provides self-contained visual cues to aid in docking. Similar to devices used to guide pilots in landing on aircraft carriers. Positions and directions of beams of light give observer visual cues of position relative to docking target point. Optical assemblies generate directed, diverging beams of light that, together, mark approach path to docking point. Conceived for use in docking spacecraft at Space Station Freedom, device adapted to numerous industrial docking and alignment applications.

  11. Enabling Exploration Through Docking Standards

    Science.gov (United States)

    Hatfield, Caris A.

    2012-01-01

    Human exploration missions beyond low earth orbit will likely require international cooperation in order to leverage limited resources. International standards can help enable cooperative missions by providing well understood, predefined interfaces allowing compatibility between unique spacecraft and systems. The International Space Station (ISS) partnership has developed a publicly available International Docking System Standard (IDSS) that provides a solution to one of these key interfaces by defining a common docking interface. The docking interface provides a way for even dissimilar spacecraft to dock for exchange of crew and cargo, as well as enabling the assembly of large space systems. This paper provides an overview of the key attributes of the IDSS, an overview of the NASA Docking System (NDS), and the plans for updating the ISS with IDSS compatible interfaces. The NDS provides a state of the art, low impact docking system that will initially be made available to commercial crew and cargo providers. The ISS will be used to demonstrate the operational utility of the IDSS interface as a foundational technology for cooperative exploration.

  12. Docking of B-cell epitope antigen to specific hepatitis B antibody

    Indian Academy of Sciences (India)

    R Rajkannan; E J Padma Malar

    2007-09-01

    The interaction of pres1 region of hepatitis B virus B-cell epitope antigen with specific hepatitis B neutralizing monoclonal antibody was examined by docking study. We modelled the 3D complex structure of B-cell epitope antigen residues CTTPAQGNSMFPSCCCTKPTDGNCY by homology modelling and docked it with the crystal structure of monoclonal antibody specific for the pres1 region of the hepatitis B virus. At the optimized docked conformation, the interactions between the amino acids of antigen and antibody were examined. It is found that the docked complex is stabilized by 59.3 kcal/mol. The stability of the docked antigen-antibody complex is due to hydrogen bonding and van der Waals interactions. The amino acids of the antigen and antibody responsible for the interaction were identified.

  13. Biological evaluation of 153Sm and 166Ho complexes with macrocyclic ligands containing acetate pendant arms as potential agents for therapy

    International Nuclear Information System (INIS)

    For the development of therapeutic radiopharmaceuticals it is essential to choose the appropriate beta-emitter as well as the carrier biomolecule. Different carrier biomolecules, namely antibodies and peptides, have been linked to different beta-emitters (153Sm, 166Ho and 177Lu) using tetraaza macrocycles as bifunctional chelators. The cavity size of these chelators, the rigidity of the macrocyclic backbone and the nature of the pendant arms seems to play an important role on the thermodynamic stability and kinetic inertness of the radiocomplexes and on their biological behaviour. In our research group we have been exploring the possibility of using tetraazamacrocycles with different cavity size, pendant arms and rigidity for preparing 153Sm and 166Ho complexes useful for therapeutical applications and/or bone pain palliation. In this communication we present the results obtained when we reacted trita and teta with 153Sm and 166Ho. The complexes are formed in good yields (> 98%), are hydrophilic and present an overall negative charges, as well as low plasmatic protein binding. Good in vitro stability in physiological media and human serum was also found for all the complexes. The biodistribution studies in mice are also presented and have shown that 153Sm/166Ho-trita and 166Ho-teta have rapid tissue clearance, comparably to the corresponding dota complexes. In contrast, 153Sm-teta has a significant lower total excretion and a significant liver and muscle uptake. Our results indicate that 153Sm/166Ho-trita form very stable complexes in vivo. However, teta, which has a larger cavity size, forms less stable complexes with the larger ion Sm3+. The biological profile of 153Sm/166Ho-trita is very interesting for the evaluation of these complexes as therapeutical agents when conjugated to biomolecules

  14. CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs

    DEFF Research Database (Denmark)

    Merveille, Anne-Christine; Davis, Erica E; Becker-Heck, Anita;

    2011-01-01

    -assembly factors of axonemal dyneins, but these mutations account for only about 50% of cases of PCD. We exploited the unique properties of dog populations to positionally clone a new PCD gene, CCDC39. We found that loss-of-function mutations in the human ortholog underlie a substantial fraction of PCD cases with...... axonemal disorganization and abnormal ciliary beating. Functional analyses indicated that CCDC39 localizes to ciliary axonemes and is essential for assembly of inner dynein arms and the dynein regulatory complex....

  15. Computational modelling of protein/protein and protein/DNA docking.

    OpenAIRE

    Moont, G.

    2005-01-01

    The docking problem is to start with unbound conformations for the components of a complex, and computationally model a near-native structure for the complex. This thesis describes work in developing computer programs to tackle both protein/protein and protein/DNA docking. Empirical pair potential functions are generated from datasets of residue/residue interactions. A scoring function was parameterised and then used to screen possible complexes, generated by the global search computer algori...

  16. A DIVERSE SOCIETY, A REPRESENTATIVE MILITARY? THE COMPLEXITY OF MANAGING DIVERSITY IN THE SOUTH AFRICAN ARMED FORCES

    OpenAIRE

    Lindy Heinecken

    2011-01-01

    After providing a brief background as to why issues of diversity managementwithin armed forces have become important internationally, this article outlines thediversity challenges facing the South African National Defence Force (SANDF).The first part of the article describes how the racial, language/ethnic and genderprofile of the SANDF has changed since 1994 and the tensions this has evoked. Thesecond part provides a brief conceptual framework against which diversitymanagement in the SANDF c...

  17. CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

    Directory of Open Access Journals (Sweden)

    Sjoerd J de Vries

    Full Text Available BACKGROUND: Macromolecular complexes are the molecular machines of the cell. Knowledge at the atomic level is essential to understand and influence their function. However, their number is huge and a significant fraction is extremely difficult to study using classical structural methods such as NMR and X-ray crystallography. Therefore, the importance of large-scale computational approaches in structural biology is evident. This study combines two of these computational approaches, interface prediction and docking, to obtain atomic-level structures of protein-protein complexes, starting from their unbound components. METHODOLOGY/PRINCIPAL FINDINGS: Here we combine six interface prediction web servers into a consensus method called CPORT (Consensus Prediction Of interface Residues in Transient complexes. We show that CPORT gives more stable and reliable predictions than each of the individual predictors on its own. A protocol was developed to integrate CPORT predictions into our data-driven docking program HADDOCK. For cases where experimental information is limited, this prediction-driven docking protocol presents an alternative to ab initio docking, the docking of complexes without the use of any information. Prediction-driven docking was performed on a large and diverse set of protein-protein complexes in a blind manner. Our results indicate that the performance of the HADDOCK-CPORT combination is competitive with ZDOCK-ZRANK, a state-of-the-art ab initio docking/scoring combination. Finally, the original interface predictions could be further improved by interface post-prediction (contact analysis of the docking solutions. CONCLUSIONS/SIGNIFICANCE: The current study shows that blind, prediction-driven docking using CPORT and HADDOCK is competitive with ab initio docking methods. This is encouraging since prediction-driven docking represents the absolute bottom line for data-driven docking: any additional biological knowledge will greatly

  18. SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models

    OpenAIRE

    Sircar, Aroop; Gray, Jeffrey J.

    2010-01-01

    High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering. When a crystallographic structure of a complex is unavailable, the structure must be predicted using computational tools. In this work, we illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the re...

  19. Docking of secretory vesicles is syntaxin dependent.

    Directory of Open Access Journals (Sweden)

    Heidi de Wit

    Full Text Available Secretory vesicles dock at the plasma membrane before they undergo fusion. Molecular docking mechanisms are poorly defined but believed to be independent of SNARE proteins. Here, we challenged this hypothesis by acute deletion of the target SNARE, syntaxin, in vertebrate neurons and neuroendocrine cells. Deletion resulted in fusion arrest in both systems. No docking defects were observed in synapses, in line with previous observations. However, a drastic reduction in morphologically docked secretory vesicles was observed in chromaffin cells. Syntaxin-deficient chromaffin cells showed a small reduction in total and plasma membrane staining for the docking factor Munc18-1, which appears insufficient to explain the drastic reduction in docking. The sub-membrane cortical actin network was unaffected by syntaxin deletion. These observations expose a docking role for syntaxin in the neuroendocrine system. Additional layers of regulation may have evolved to make syntaxin redundant for docking in highly specialized systems like synaptic active zones.

  20. Cross-docking: State of the art

    OpenAIRE

    Van Belle, Jan; Valckenaers, Paul; Cattrysse, Dirk

    2012-01-01

    Cross-docking is a logistics strategy in which freight is unloaded from inbound vehicles and (almost) directly loaded into outbound vehicles, with little or no storage in between. This article presents an overview of the cross-docking concept. Guidelines for the successful use and implementation of cross-docking are discussed and several characteristics are described that can be used to distinguish between different cross-dock types. In addition, this article presents an extensive review of t...

  1. ASPDock: protein-protein docking algorithm using atomic solvation parameters model

    Directory of Open Access Journals (Sweden)

    Liu Shiyong

    2011-01-01

    Full Text Available Abstract Background Atomic Solvation Parameters (ASP model has been proven to be a very successful method of calculating the binding free energy of protein complexes. This suggests that incorporating it into docking algorithms should improve the accuracy of prediction. In this paper we propose an FFT-based algorithm to calculate ASP scores of protein complexes and develop an ASP-based protein-protein docking method (ASPDock. Results The ASPDock is first tested on the 21 complexes whose binding free energies have been determined experimentally. The results show that the calculated ASP scores have stronger correlation (r ≈ 0.69 with the binding free energies than the pure shape complementarity scores (r ≈ 0.48. The ASPDock is further tested on a large dataset, the benchmark 3.0, which contain 124 complexes and also shows better performance than pure shape complementarity method in docking prediction. Comparisons with other state-of-the-art docking algorithms showed that ASP score indeed gives higher success rate than the pure shape complementarity score of FTDock but lower success rate than Zdock3.0. We also developed a softly restricting method to add the information of predicted binding sites into our docking algorithm. The ASP-based docking method performed well in CAPRI rounds 18 and 19. Conclusions ASP may be more accurate and physical than the pure shape complementarity in describing the feature of protein docking.

  2. Finding correct protein–protein docking models using ProQDock

    Science.gov (United States)

    Basu, Sankar; Wallner, Björn

    2016-01-01

    Motivation: Protein–protein interactions are a key in virtually all biological processes. For a detailed understanding of the biological processes, the structure of the protein complex is essential. Given the current experimental techniques for structure determination, the vast majority of all protein complexes will never be solved by experimental techniques. In lack of experimental data, computational docking methods can be used to predict the structure of the protein complex. A common strategy is to generate many alternative docking solutions (atomic models) and then use a scoring function to select the best. The success of the computational docking technique is, to a large degree, dependent on the ability of the scoring function to accurately rank and score the many alternative docking models. Results: Here, we present ProQDock, a scoring function that predicts the absolute quality of docking model measured by a novel protein docking quality score (DockQ). ProQDock uses support vector machines trained to predict the quality of protein docking models using features that can be calculated from the docking model itself. By combining different types of features describing both the protein–protein interface and the overall physical chemistry, it was possible to improve the correlation with DockQ from 0.25 for the best individual feature (electrostatic complementarity) to 0.49 for the final version of ProQDock. ProQDock performed better than the state-of-the-art methods ZRANK and ZRANK2 in terms of correlations, ranking and finding correct models on an independent test set. Finally, we also demonstrate that it is possible to combine ProQDock with ZRANK and ZRANK2 to improve performance even further. Availability and implementation: http://bioinfo.ifm.liu.se/ProQDock Contact: bjornw@ifm.liu.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307625

  3. Hydra Rendezvous and Docking Sensor

    Science.gov (United States)

    Roe, Fred; Carrington, Connie

    2007-01-01

    The U.S. technology to support a CEV AR&D activity is mature and was developed by NASA and supporting industry during an extensive research and development program conducted during the 1990's and early 2000 time frame at the Marshall Space Flight Center. Development and demonstration of a rendezvous/docking sensor was identified early in the AR&D Program as the critical enabling technology that allows automated proxinity operations and docking. A first generation rendezvous/docking sensor, the Video Guidance Sensor (VGS) was developed and successfully flown on STS 87 and again on STS 95, proving the concept of a video-based sensor. Advances in both video and signal processing technologies and the lessons learned from the two successful flight experiments provided a baseline for the development of a new generation of video based rendezvous/docking sensor. The Advanced Video Guidance Sensor (AVGS) has greatly increased performance and additional capability for longer-range operation. A Demonstration Automatic Rendezvous Technology (DART) flight experiment was flown in April 2005 using AVGS as the primary proximity operations sensor. Because of the absence of a docking mechanism on the target satellite, this mission did not demonstrate the ability of the sensor to coltrold ocking. Mission results indicate that the rendezvous sensor operated successfully in "spot mode" (2 km acquisition of the target, bearing data only) but was never commanded to "acquire and track" the docking target. Parts obsolescence issues prevent the construction of current design AVGS units to support the NASA Exploration initiative. This flight proven AR&D technology is being modularized and upgraded with additional capabilities through the Hydra project at the Marshall Space Flight Center. Hydra brings a unique engineering approach and sensor architecture to the table, to solve the continuing issues of parts obsolescence and multiple sensor integration. This paper presents an approach to

  4. The Asteroid Redirect Mission (ARM)

    Science.gov (United States)

    Abell, Paul; Gates, Michele; Johnson, Lindley; Chodas, Paul; Mazanek, Dan; Reeves, David; Ticker, Ronald

    2016-07-01

    To achieve its long-term goal of sending humans to Mars, the National Aeronautics and Space Administration (NASA) plans to proceed in a series of incrementally more complex human spaceflight missions. Today, human flight experience extends only to Low-Earth Orbit (LEO), and should problems arise during a mission, the crew can return to Earth in a matter of minutes to hours. The next logical step for human spaceflight is to gain flight experience in the vicinity of the Moon. These cis-lunar missions provide a "proving ground" for the testing of systems and operations while still accommodating an emergency return path to the Earth that would last only several days. Cis-lunar mission experience will be essential for more ambitious human missions beyond the Earth-Moon system, which will require weeks, months, or even years of transit time. In addition, NASA has been given a Grand Challenge to find all asteroid threats to human populations and know what to do about them. Obtaining knowledge of asteroid physical properties combined with performing technology demonstrations for planetary defense provide much needed information to address the issue of future asteroid impacts on Earth. Hence the combined objectives of human exploration and planetary defense give a rationale for the Asteroid Re-direct Mission (ARM). Mission Description: NASA's ARM consists of two mission segments: 1) the Asteroid Redirect Robotic Mission (ARRM), the first robotic mission to visit a large (greater than ~100 m diameter) near-Earth asteroid (NEA), collect a multi-ton boulder from its surface along with regolith samples, demonstrate a planetary defense technique, and return the asteroidal material to a stable orbit around the Moon; and 2) the Asteroid Redirect Crewed Mission (ARCM), in which astronauts will take the Orion capsule to rendezvous and dock with the robotic vehicle, conduct multiple extravehicular activities to explore the boulder, and return to Earth with samples. NASA's proposed

  5. Robotic arm

    Science.gov (United States)

    Kwech, Horst

    1989-04-18

    A robotic arm positionable within a nuclear vessel by access through a small diameter opening and having a mounting tube supported within the vessel and mounting a plurality of arm sections for movement lengthwise of the mounting tube as well as for movement out of a window provided in the wall of the mounting tube. An end effector, such as a grinding head or welding element, at an operating end of the robotic arm, can be located and operated within the nuclear vessel through movement derived from six different axes of motion provided by mounting and drive connections between arm sections of the robotic arm. The movements are achieved by operation of remotely-controllable servo motors, all of which are mounted at a control end of the robotic arm to be outside the nuclear vessel.

  6. Robotic arm

    International Nuclear Information System (INIS)

    A robotic arm positionable within a nuclear vessel by access through a small diameter opening and having a mounting tube supported within the vessel and mounting a plurality of arm sections for movement lengthwise of the mounting tube as well as for movement out of a window provided in the wall of the mounting tube is disclosed. An end effector, such as a grinding head or welding element, at an operating end of the robotic arm, can be located and operated within the nuclear vessel through movement derived from six different axes of motion provided by mounting and drive connections between arm sections of the robotic arm. The movements are achieved by operation of remotely-controllable servo motors, all of which are mounted at a control end of the robotic arm to be outside the nuclear vessel. 23 figs

  7. Syntheses, structural variations and fluorescence studies of two dinuclear zinc(II) complexes of a Schiff base ligand with an extended carboxylate side arm

    Science.gov (United States)

    Shit, Shyamapada; Sasmal, Ashok; Dhal, Piu; Rizzoli, Corrado; Mitra, Samiran

    2016-03-01

    A potentially tetradentate Schiff base ligand containing carboxylic acid group, HL, (E)-2-((pyridin-2-yl)methyleneamino)-5-chlorobenzoic acid is synthesized and characterized. Reaction of HL with hydrated zinc(II) trichloroacetate and zinc(II) trifluoroacetate under similar reaction condition yields two discrete dinuclear complexes, [Zn(L)(Cl)]2 (1) and [Zn(L)(CF3COO)]2 (2) and characterized by different physicochemical methods. Single crystal X-ray structural characterization reveals different ligating properties of the coordinated anionic ligand (L-) in its zinc(II) complexes. The side arm carboxylate of L- shows μ1,3-carboxylato-bridging mode in 1 and connects zinc(II) atoms in syn-anti fashion while it exhibits a μ1,1-carboxylato-bridging mode in 2. The metal ions display distorted square pyramidal geometries in both the structures and associated with different degrees of distortions. The fluorescence spectra of HL and its zinc(II) complexes recorded in methanol at room temperature which reveal the enhancement of emission intensity for the complexes compared to that of the free ligand. Thermogravimetric analyses (TGA) reveal high thermal stabilities of the complexes.

  8. Flexible Docking of Proteins and "Drug-like" Ligands.

    Science.gov (United States)

    Tang, Hai-Xu; Ye, Yu-Zhen; Ding, Da-Fu

    1998-01-01

    By using "tabu search" algorithm and Gehlhaar potential function, a new approach is presented for flexible docking of protein and its "drug-like" ligand has been developed. Computational test for this method with a set of 100 complexes has been performed, which indicated that the deviation of 89% of the predicted complex conformation was less than 0.25 nm. Compared with GOLD, a program of genetic algorithm, our method has high accuracy, low limit and short computation time. PMID:12168000

  9. Vehicle routing with cross-docking

    DEFF Research Database (Denmark)

    Wen, Min; Larsen, Jesper; Clausen, Jens; Cordeau, Jean-Francois; Laporte, Gilbert

    2009-01-01

    Over the past decade, cross-docking has emerged as an important material handling technology in transportation. A variation of the well-known Vehicle Routing Problem (VRP), the VRP with Cross-Docking (VRPCD) arises in a number of logistics planning contexts. This paper addresses the VRPCD, where a...... set of homogeneous vehicles are used to transport orders from the suppliers to the corresponding customers via a cross-dock. The orders can be consolidated at the cross-dock but cannot be stored for very long because the cross-dock does not have long-term inventory-holding capabilities. The objective...

  10. Synthesis and characterization of ethylbis(2-pyridylethyl)amineruthenium complexes and two different types of C-H bond cleavage at an ethylene arm.

    Science.gov (United States)

    Fukui, Sohei; Kajihara, Akari; Hirano, Toshiyuki; Sato, Fumitoshi; Suzuki, Noriyuki; Nagao, Hirotaka

    2011-06-01

    Ruthenium complexes bearing ethylbis(2-pyridylethyl)amine (ebpea), which has flexible -C(2)H(4)- arms between the amine and the pyridyl groups and coordinates to a metal center in facial and meridional modes, have been synthesized and characterized. Three trichloro complexes, fac-[Ru(III)Cl(3)(ebpea)] (fac-[1]), mer-[Ru(III)Cl(3)(ebpea)] (mer-[1]), and mer-[Ru(II)Cl(3){η(2)-N(C(2)H(5))(C(2)H(4)py)═CH-CH(2)py}] (mer-[2]), were synthesized using the Ru blue solution. Formation of mer-[2] proceeded via a C-H activation of the CH(2) group next to the amine nitrogen atom of the ethylene arm. Reduction reactions of fac- and mer-[1] afforded a triacetonitrile complex mer-[Ru(II)(CH(3)CN)(3)(ebpea)](PF(6))(2) (mer-[3](PF(6))(2)). Five nitrosyl complexes fac-[RuX(2)(NO)(ebpea)]PF(6) (X = Cl for fac-[4]PF(6); X = ONO(2) for fac-[5]PF(6)) and mer-[RuXY(NO)(ebpea)]PF(6) (X = Cl, Y = Cl for mer-[4]PF(6); X = Cl, Y = CH(3)O for mer-[6]PF(6); X = Cl, Y = OH for mer-[7]PF(6)) were synthesized and characterized by X-ray crystallography. A reaction of mer-[2] in H(2)O-C(2)H(5)OH at room temperature afforded mer-[1]. Oxidation of C(2)H(5)OH in H(2)O-C(2)H(5)OH and i-C(3)H(7)OH in H(2)O-i-C(3)H(7)OH to acetaldehyde and acetone by mer-[2] under stirring at room temperature occurred with formation of mer-[1]. Alternative C-H activation of the CH(2) group occurred next to the pyridyl group, and formation of a C-N bond between the CH moiety and the nitrosyl ligand afforded a nitroso complex [Ru(II)(N(3))(2){N(O)CH(py)CH(2)N(C(2)H(5))C(2)H(4)py}] ([8]) in reactions of nitrosyl complexes with sodium azide in methanol, and reaction of [8] with hydrochloric acid afforded a corresponding chloronitroso complex [Ru(II)Cl(2){N(O)CH(py)CH(2)N(C(2)H(5))C(2)H(4)py}] ([9]). PMID:21517051

  11. A DIVERSE SOCIETY, A REPRESENTATIVE MILITARY? THE COMPLEXITY OF MANAGING DIVERSITY IN THE SOUTH AFRICAN ARMED FORCES

    Directory of Open Access Journals (Sweden)

    Lindy Heinecken

    2011-08-01

    Full Text Available After providing a brief background as to why issues of diversity managementwithin armed forces have become important internationally, this article outlines thediversity challenges facing the South African National Defence Force (SANDF.The first part of the article describes how the racial, language/ethnic and genderprofile of the SANDF has changed since 1994 and the tensions this has evoked. Thesecond part provides a brief conceptual framework against which diversitymanagement in the SANDF can be interpreted, whereafter the various diversitymanagement programmes instituted over the years to cultivate a respect for diversityare outlined. It is argued that the predominant emphasis on ‘workplace diversity’ atthe cost of ‘valuing diversity’ has meant that existing stereotypes and tensionswithin the ranks have remained, with dire consequences not only for thecohesiveness and effectiveness of the SANDF, but also for civil-military relations.

  12. Chunk concatenation evolves with practice and sleep-related enhancement consolidation in a complex arm movement sequence

    Directory of Open Access Journals (Sweden)

    Blischke Klaus

    2016-06-01

    Full Text Available This paper addresses the notion of chunk concatenation being associated with sleep-related enhancement consolidation of motor sequence memory, thereby essentially contributing to improvements in sequence execution speed. To this end, element movement times of a multi-joint arm movement sequence incorporated in a recent study by Malangré et al. (2014 were reanalyzed. As sequence elements differed with respect to movement distance, element movement times had to be purged from differences solely due to varying trajectory lengths. This was done by dividing each element movement time per subject and trial block by the respective “reference movement time” collected from subjects who had extensively practiced each sequence element in isolation. Any differences in these “relative element movement times” were supposed to reflect element-specific “production costs” imposed solely by the sequence context. Across all subjects non-idiosyncratic, lasting sequence segmentation was shown, and four possible concatenation points (i.e. transition points between successive chunks within the original arm movement sequence were identified. Based on theoretical suppositions derived from previous work with the discrete sequence production task and the dual processor model (Abrahamse et al., 2013, significantly larger improvements in transition speed occurring at these four concatenation points as compared to the five fastest transition positions within the sequence (associated with mere element execution were assumed to indicate increased chunk concatenation. As a result, chunk concatenation was shown to proceed during acquisition with physical practice, and, most importantly, to significantly progress some more during retention following a night of sleep, but not during a waking interval.

  13. Antibacterial, DNA interaction and cytotoxic activities of pendant-armed polyamine macrocyclic dinuclear nickel(II) and copper(II) complexes

    Science.gov (United States)

    Arthi, P.; Haleel, A.; Srinivasan, P.; Prabhu, D.; Arulvasu, C.; Kalilur Rahiman, A.

    2014-08-01

    A series of dinuclear nickel(II) and copper(II) complexes (1-6) of hexaaza macrocycles of 2,6-diformyl-4-methylphenol with three different benzoyl pendant-arms, 2,2‧-benzoyliminodi(ethylamine) trihydrochloride (L), 2,2‧-4-nitrobenzoyliminodi(ethylamine) trihydrochloride (L‧) and 2,2‧-3,5-dinitrobenzoyliminodi(ethylamine) trihydrochloride (L″) have been synthesized and characterized by spectral methods. The electrochemical studies of these complexes depict two irreversible one electron reduction processes around E1pc = -0.62 to -0.76 V and E2pc = -1.21 to -1.31, and nickel(II) complexes (1-3) exhibit two irreversible one electron oxidation processes around E1pa = 1.08 to 1.14 V and E2pa = 1.71 to 1.74 V. The room temperature magnetic moment values (μeff, 1.52-1.54 BM) indicate the presence of an antiferromagnetic interaction in the binuclear copper(II) complexes (4-6) which is also observed from the broad ESR spectra with a g value of 2.14-2.15. The synthesized complexes (1-6) were screened for their antibacterial activity. The results of DNA interaction studies indicate that the dinuclear complexes can bind to calf thymus DNA by intercalative mode and display efficient cleavage of plasmid DNA. Further, the cytotoxic activity of complexes 2, 5 and 6 on human liver adenocarcinoma (HepG2) cell line has been examined. Nuclear-chromatin cleavage has also been observed with PI staining and comet assays.

  14. Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms.

    Science.gov (United States)

    Hanawa-Suetsugu, Kyoko; Kukimoto-Niino, Mutsuko; Mishima-Tsumagari, Chiemi; Akasaka, Ryogo; Ohsawa, Noboru; Sekine, Shun-ichi; Ito, Takuhiro; Tochio, Naoya; Koshiba, Seizo; Kigawa, Takanori; Terada, Takaho; Shirouzu, Mikako; Nishikimi, Akihiko; Uruno, Takehito; Katakai, Tomoya; Kinashi, Tatsuo; Kohda, Daisuke; Fukui, Yoshinori; Yokoyama, Shigeyuki

    2012-02-28

    DOCK2, a hematopoietic cell-specific, atypical guanine nucleotide exchange factor, controls lymphocyte migration through ras-related C3 botulinum toxin substrate (Rac) activation. Dedicator of cytokinesis 2-engulfment and cell motility protein 1 (DOCK2•ELMO1) complex formation is required for DOCK2-mediated Rac signaling. In this study, we identified the N-terminal 177-residue fragment and the C-terminal 196-residue fragment of human DOCK2 and ELMO1, respectively, as the mutual binding regions, and solved the crystal structure of their complex at 2.1-Å resolution. The C-terminal Pro-rich tail of ELMO1 winds around the Src-homology 3 domain of DOCK2, and an intermolecular five-helix bundle is formed. Overall, the entire regions of both DOCK2 and ELMO1 assemble to create a rigid structure, which is required for the DOCK2•ELMO1 binding, as revealed by mutagenesis. Intriguingly, the DOCK2•ELMO1 interface hydrophobically buries a residue which, when mutated, reportedly relieves DOCK180 from autoinhibition. We demonstrated that the ELMO-interacting region and the DOCK-homology region 2 guanine nucleotide exchange factor domain of DOCK2 associate with each other for the autoinhibition, and that the assembly with ELMO1 weakens the interaction, relieving DOCK2 from the autoinhibition. The interactions between the N- and C-terminal regions of ELMO1 reportedly cause its autoinhibition, and binding with a DOCK protein relieves the autoinhibition for ras homolog gene family, member G binding and membrane localization. In fact, the DOCK2•ELMO1 interface also buries the ELMO1 residues required for the autoinhibition within the hydrophobic core of the helix bundle. Therefore, the present complex structure reveals the structural basis by which DOCK2 and ELMO1 mutually relieve their autoinhibition for the activation of Rac1 for lymphocyte chemotaxis. PMID:22331897

  15. Benchmarking Sets for Molecular Docking

    OpenAIRE

    Huang, Niu; Shoichet, Brian K.; Irwin, John J.

    2006-01-01

    Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 9...

  16. Open Syntaxin Docks Synaptic Vesicles

    OpenAIRE

    Marc Hammarlund; Mark T Palfreyman; Shigeki Watanabe; Shawn Olsen; Erik M. Jorgensen

    2007-01-01

    Author Summary Like Olympic swimmers crouched on their starting blocks, synaptic vesicles prepare for fusion with the neuronal plasma membrane long before the starting gun fires. This preparation enables vesicles to fuse rapidly, synchronously, and in the correct place when the signal finally arrives. A well-known but poorly understood part of vesicle preparation is docking, in which vesicles prepare for release by attaching to the plasma membrane at the eventual site of release. Here, we out...

  17. Uranyl complexes formed with a para-t-butylcalix[4]arene bearing phosphinoyl pendant arms on the lower rim. Solid and solution studies

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, F. de M. [Instituto Nacional de Investigaciones Nucleares, La Marquesa, Ocoyoacac (Mexico). Dept. de Quimica; Varbanov, S. [Bulgarian Academy of Sciences, Sofia (Bulgaria). Inst. of Organic Chemistry with Center of Phytochemistry; Buenzli, J.C.G. [Ecole Polytechnique Federale de Lausanne (EPFL) (Switzerland). Inst. of Chemical Sciences and Engineering; Rivas-Silva, J.F.; Ocana-Bribiesca, M.A. [Instituto de Fisica de la BUAP, Puebla (Mexico); Cortes-Jacome, M.A.; Toledo-Antonio, J.A. [Instituto Mexicano del Petroleo/Programa de Ingenieria Molecular (Mexico)

    2012-07-01

    The current interest in functionalized calixarenes with phosphorylated pendant arms resides in their coordination ability towards f elements and capability towards actinide/rare earth separation. Uranyl cation forms 1:1 and 1:2 (M:L) complexes with a tetra-phosphinoylated p-tert-butylcalix[4]arene, B{sub 4}bL{sup 4}: UO{sub 2}(NO{sub 3}){sub 2}(B{sub 4}bL{sup 4}){sub n} . xH{sub 2}O (n = 1, x = 2, 1; n = 2, x = 6, 2). Spectroscopic data point to the inner coordination sphere of 1 containing one monodentate nitrate anion, one water molecule and the four phosphinoylated arms bound to UO{sub 2}{sup 2+} while in 2, uranyl is only coordinated to calixarene ligands. In both cases the U(VI) ion is 8-coordinate. Uranyl complexes display enhanced metal-centred luminescence due to energy transfer from the calixarene ligands; the luminescence decays are bi-exponential with associated lifetimes in the ranges 220 {mu}s < {tau}{sub s} < 250 {mu}s and 630 {mu}s < {tau}{sub L} < 640 {mu}s, pointing to the presence of two species with differently coordinated calixarene, as substantiated by a XPS study of U(4f{sub 5/2,7/2}), O(1s) and P(2p) levels on solid state samples. The extraction study of UO{sub 2}{sup 2+} cation and trivalent rare-earth (Y, La, Eu) ions from acidic nitrate media by B{sub 4}bL{sup 4} in chloroform shows the uranyl cation being much more extracted than rare earths. (orig.)

  18. A diamine ligand with long 'arms' and its corresponding dinuclear rhenium(I) complex: Synthesis, characterization, photophysical property, and sensing activity towards molecular oxygen

    Energy Technology Data Exchange (ETDEWEB)

    Xu Xiaoyong, E-mail: dreamxxy01@163.com [Center for Functional Materials of Pingxiang, Pingxiang 337055 (China) and College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Xiao Hanning [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China)

    2012-09-15

    In this paper, we synthesize a novel diamine ligand of 4,7-dinonadecyl-1,10-phenanthroline (DN-Phen) with two long alkyl chain arms serving as a shield and its corresponding dinuclear Re(I) complex of Re{sub 2}(CO){sub 6}(bpy)(DN-Phen){sub 2} (bpy=4,4 Prime -bipyridine), aiming at an optical sensor immune to the surrounding interferences. Its geometric and electronic structures are investigated, which suggest that the introduced long alkyl chains act as a shield for the excited state of emissive center. The promising photophysical parameters of Re{sub 2}(CO){sub 6}(bpy)(DN-Phen){sub 2}, including the immunity of emission towards the surrounding interferences and long excited state lifetime, make itself a potential probe for oxygen detection. By doping Re{sub 2}(CO){sub 6}(bpy)(DN-Phen){sub 2} into two silica matrixes of MCM-41 and SBA-15, oxygen sensing performances of the resulted composite materials are investigated. Finally, a high sensitivity of 20.1 is realized, with short response/recovery time of 8 s/42 s. Here, sensitivity is defined as the ratio of emission maximum under pure nitrogen to emission minimum under pure oxygen, response and recovery times are the times for a sample to lose (response time) or recover (recovery time) 95% of its emission maximum upon periodically changed atmosphere. - Highlights: Black-Right-Pointing-Pointer A ligand with two long alkyl chain arms serving as a shield is synthesized. Black-Right-Pointing-Pointer The shield protects the excited state emissive center. Black-Right-Pointing-Pointer The emission of Re(I) complex is immune towards surrounding interference. Black-Right-Pointing-Pointer A high sensitivity of 20.1 is realized.

  19. European rendezvous and docking system

    Science.gov (United States)

    Pairot, J. M.; Frezet, M.; Tailhades, J.; Fehse, W.; Tobias, A.; Getzschmann, A.

    This paper first describes the major design drivers and the key features of the European RendezVous and Docking System Concept. Stemming from technology activities led by the European Space Agency (ESA) with European Industry and National Space Agencies since the beginning of the eighties, the concept has been developed and integrated in the frame of an ESA RVD System Pre-Development Programme initiated at ESTEC in 1989, with MATRA as main contractor. The objective is to verify the overall concept and the main elements within a RVD Proof of Concept Programme in order to provide an early proof of validity to the user projects, the first of which will be the Hermes manned space shuttle. The selected mission scenarii, the RVD functions addressed and the overall system architecture are described. The results of supporting safety, performance and operations analyses are presented. The paper further presents the verification objectives and the major results obtained in the RVD System Pre-Development Programme. This verification approach involves hardware breadboards, software prototypes, development of test facilities in four main development areas: test of RV sensors on a 6 d.o.f. kinematic test facility, test of a docking mechanism front-end mock-up on the docking dynamics test facility, closed-loop test of a prototype RV control software, test of man-in-the-loop concept involving both supervisory control and manual control modes.

  20. Molecular Docking of Aromatase Inhibitors

    Directory of Open Access Journals (Sweden)

    Virapong Prachayasittikul

    2011-04-01

    Full Text Available Aromatase is an enzyme that plays a critical role in the development of estrogen receptor positive breast cancer. As aromatase catalyzes the aromatization of androstenedione to estrone, a naturally occurring estrogen, it is a promising drug target for therapeutic management. The undesirable effects found in aromatase inhibitors (AIs that are in clinical use necessitate the discovery of novel AIs with higher selectivity, less toxicity and improving potency. In this study, we elucidate the binding mode of all three generations of AI drugs to the crystal structure of aromatase by means of molecular docking. It was demonstrated that the docking protocol could reliably reproduce the interaction of aromatase with its substrate with an RMSD of 1.350 Å. The docking study revealed that polar (D309, T310, S478 and M374, aromatic (F134, F221 and W224 and non-polar (A306, A307, V370, L372 and L477 residues were important for interacting with the AIs. The insights gained from the study herein have great potential for the design of novel AIs.

  1. PaFlexPepDock: parallel ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta.

    Directory of Open Access Journals (Sweden)

    Haiou Li

    Full Text Available Structural information related to protein-peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein-peptide interactions explored by experimental ways. Protein-peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein-peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein-peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.

  2. Why are most EU pigs tail docked?

    DEFF Research Database (Denmark)

    D'eath, R.B.; Niemi, J.K.; Vosough Ahmadi, B.;

    2016-01-01

    To limit tail biting incidence, most pig producers in Europe tail dock their piglets. This is despite EU Council Directive 2008/120/EC banning routine tail docking and allowing it only as a last resort. The paper aims to understand what it takes to fulfil the intentions of the Directive by...... pig per day) and no tail docking. A decision tree model based on data from Danish and Finnish pig production suggests that Standard Docked provides the highest economic gross margin with the least tail biting. Given our assumptions, Enhanced Undocked is the least economic, although Efficient Undocked...... is better economically and both result in a lower incidence of tail biting than Standard Undocked but higher than Standard Docked. For a pig, being bitten is worse for welfare (repeated pain, risk of infections) than being docked, but to compare welfare consequences at a farm level means considering...

  3. Combination of scoring schemes for protein docking

    Directory of Open Access Journals (Sweden)

    Schomburg Dietmar

    2007-08-01

    Full Text Available Abstract Background Docking algorithms are developed to predict in which orientation two proteins are likely to bind under natural conditions. The currently used methods usually consist of a sampling step followed by a scoring step. We developed a weighted geometric correlation based on optimised atom specific weighting factors and combined them with our previously published amino acid specific scoring and with a comprehensive SVM-based scoring function. Results The scoring with the atom specific weighting factors yields better results than the amino acid specific scoring. In combination with SVM-based scoring functions the percentage of complexes for which a near native structure can be predicted within the top 100 ranks increased from 14% with the geometric scoring to 54% with the combination of all scoring functions. Especially for the enzyme-inhibitor complexes the results of the ranking are excellent. For half of these complexes a near-native structure can be predicted within the first 10 proposed structures and for more than 86% of all enzyme-inhibitor complexes within the first 50 predicted structures. Conclusion We were able to develop a combination of different scoring schemes which considers a series of previously described and some new scoring criteria yielding a remarkable improvement of prediction quality.

  4. Scheduling Trucks in a Cross-Dock with Mixed Service Mode Dock Doors

    DEFF Research Database (Denmark)

    Bodnar, Peter; Azadeh, Kaveh; Koster, René de

    2015-01-01

    The problem considered in this paper is how to schedule inbound and outbound trucks subject to time windows at a multidoor cross-dock. Dock doors can either be dedicated to inbound or outbound trucks or be capable of handling both truck types. In addition, loads are allowed to be temporarily buff...... problems of four warehouses of a large retailer and show that substantially smaller cross-docks can be used by using dock-doors flexibly and properly scheduling the trucks....

  5. Machine learning optimization of cross docking accuracy.

    Science.gov (United States)

    Bjerrum, Esben J

    2016-06-01

    Performance of small molecule automated docking programs has conceptually been divided into docking -, scoring -, ranking - and screening power, which focuses on the crystal pose prediction, affinity prediction, ligand ranking and database screening capabilities of the docking program, respectively. Benchmarks show that different docking programs can excel in individual benchmarks which suggests that the scoring function employed by the programs can be optimized for a particular task. Here the scoring function of Smina is re-optimized towards enhancing the docking power using a supervised machine learning approach and a manually curated database of ligands and cross docking receptor pairs. The optimization method does not need associated binding data for the receptor-ligand examples used in the data set and works with small train sets. The re-optimization of the weights for the scoring function results in a similar docking performance with regard to docking power towards a cross docking test set. A ligand decoy based benchmark indicates a better discrimination between poses with high and low RMSD. The reported parameters for Smina are compatible with Autodock Vina and represent ready-to-use alternative parameters for researchers who aim at pose prediction rather than affinity prediction. PMID:27179709

  6. Protein-protein docking using region-based 3D Zernike descriptors

    Directory of Open Access Journals (Sweden)

    Sael Lee

    2009-12-01

    Full Text Available Abstract Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for

  7. Modeling of metal interaction geometries for protein-ligand docking.

    Science.gov (United States)

    Seebeck, Birte; Reulecke, Ingo; Kämper, Andreas; Rarey, Matthias

    2008-05-15

    The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. PMID:18041759

  8. Crusader Automated Docking System: Technology support for the Crusader Resupply Team. Interim report, Ammunition Logistics Program

    Energy Technology Data Exchange (ETDEWEB)

    Kring, C.T.; Varma, V.K.; Jatko, W.B.

    1995-11-01

    The US Army and Team Crusader (United Defense, Lockheed Martin Armament Systems, etc.) are developing the next generation howitzer, the Crusader. The development program includes an advanced, self-propelled liquid propellant howitzer and a companion resupply vehicle. The resupply vehicle is intended to rendezvous with the howitzer near the battlefront and replenish ammunition, fuel, and other material. The Army has recommended that Crusader incorporate new and innovative technologies to improve performance and safety. One conceptual design proposes a robotic resupply boom on the resupply vehicle to upload supplies to the howitzer. The resupply boom would normally be retracted inside the resupply vehicle during transit. When the two vehicles are within range of the resupply boom, the boom would be extended to a receiving port on the howitzer. In order to reduce exposure to small arms fire or nuclear, biological, and chemical hazards, the crew would remain inside the resupply vehicle during the resupply operation. The process of extending the boom and linking with the receiving port is called docking. A boom operator would be designated to maneuver the boom into contact with the receiving port using a mechanical joystick. The docking operation depends greatly upon the skill of the boom operator to manipulate the boom into docking position. Computer simulations at the National Aeronautics and Space Administration have shown that computer-assisted or autonomous docking can improve the ability of the operator to dock safely and quickly. This document describes the present status of the Crusader Autonomous Docking System (CADS) implemented at Oak Ridge National laboratory (ORNL). The purpose of the CADS project is to determine the feasibility and performance limitations of vision systems to satisfy the autonomous docking requirements for Crusader and conduct a demonstration under controlled conditions.

  9. DockAnalyse: an application for the analysis of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Cedano Juan

    2010-10-01

    Full Text Available Abstract Background Is it possible to identify what the best solution of a docking program is? The usual answer to this question is the highest score solution, but interactions between proteins are dynamic processes, and many times the interaction regions are wide enough to permit protein-protein interactions with different orientations and/or interaction energies. In some cases, as in a multimeric protein complex, several interaction regions are possible among the monomers. These dynamic processes involve interactions with surface displacements between the proteins to finally achieve the functional configuration of the protein complex. Consequently, there is not a static and single solution for the interaction between proteins, but there are several important configurations that also have to be analyzed. Results To extract those representative solutions from the docking output datafile, we have developed an unsupervised and automatic clustering application, named DockAnalyse. This application is based on the already existing DBscan clustering method, which searches for continuities among the clusters generated by the docking output data representation. The DBscan clustering method is very robust and, moreover, solves some of the inconsistency problems of the classical clustering methods like, for example, the treatment of outliers and the dependence of the previously defined number of clusters. Conclusions DockAnalyse makes the interpretation of the docking solutions through graphical and visual representations easier by guiding the user to find the representative solutions. We have applied our new approach to analyze several protein interactions and model the dynamic protein interaction behavior of a protein complex. DockAnalyse might also be used to describe interaction regions between proteins and, therefore, guide future flexible dockings. The application (implemented in the R package is accessible.

  10. No dry dock: safely strategy for avoiding unplanned dry dock and reducing safety, health and environment risks

    Energy Technology Data Exchange (ETDEWEB)

    Constantinis, Danny A.; Brett, David E. [EM and I Alliance, Cheshire (United Kingdom)

    2012-07-01

    There are currently over 150 operational FPUs with an expected increase of a further 100 units in the next 5 years. This results from several factors: increasing demand for hydrocarbons; new reserves in deep water; pipeline infrastructure is not required and FPU design fits many field requirements. FPUs are increasingly chosen for large, deep water, longer life developments. Units are bigger and more complex. Regulators and oil majors are imposing more stringent integrity requirements to protect against safety, environmental and operational risks related to loss of containment and loss of hull structure integrity which could lead to HSE risks, increased costs and production losses which would become particularly onerous should the unit have to dry dock. There are a number of other important components the context of asset integrity, e.g. mooring and sub sea systems, but these are outside the scope of this paper. The 'No Dry dock....Safely' approach is based on the principle of Criticality Based Integrity which identifies components whose integrity is critical to avoiding incidents and the risk of dry docking. Once critical components are identified the challenge is to establish integrity status and maintain fitness-for-service. Various JIPs e.g. the Hull Inspection Techniques and Strategies are looking at best practice inspection methodologies. The industry is progressing ways of maintaining and repairing critical items without going to dry dock. The challenges include coating maintenance, structural and pressure system repairs. Advances in cathodic protection and coating maintenance strategies are proving successful as are techniques for carrying out major structural repairs. The 'No Dry dock...Safely' methodology is a proven solution and case histories have been included. Technological advances will further improve integrity in the industry. There is no reason why FPUs cannot be kept on station and in production for 25 years or more whilst

  11. A Review on Quantitative Approaches for Dock Door Assignment in Cross-Docking

    Directory of Open Access Journals (Sweden)

    Adibah Shuib

    2012-01-01

    Full Text Available Cross docking is a relatively new technique in supply chain operations. It offers limited storage time to maximize the efficiency of goods transshipment. Efficient operation of a cross docking system requires an appropriate coordination of inbound and outbound flows, accurate planning and dynamic scheduling.  The planning strategies at cross docking terminals, which are receiving growing attention today, are the truck-to-door assignment and destination to door assignment problems. This paper provides a comprehensive literature review of quantitative approaches in dock door assignment problems of cross docking planning. The contributions of this paper are to identify the gap of knowledge in operational levels mainly in dock door assignment and to point out the future research direction in cross docking.

  12. Galaxy7TM: flexible GPCR-ligand docking by structure refinement.

    Science.gov (United States)

    Lee, Gyu Rie; Seok, Chaok

    2016-07-01

    G-protein-coupled receptors (GPCRs) play important physiological roles related to signal transduction and form a major group of drug targets. Prediction of GPCR-ligand complex structures has therefore important implications to drug discovery. With previously available servers, it was only possible to first predict GPCR structures by homology modeling and then perform ligand docking on the model structures. However, model structures generated without explicit consideration of specific ligands of interest can be inaccurate because GPCR structures can be affected by ligand binding. The Galaxy7TM server, freely accessible at http://galaxy.seoklab.org/7TM, improves an input GPCR structure by simultaneous ligand docking and flexible structure refinement using GALAXY methods. The server shows better performance in both ligand docking and GPCR structure refinement than commonly used programs AutoDock Vina and Rosetta MPrelax, respectively. PMID:27131365

  13. Vehicle Routing Problem for Fashion Supply Chains with Cross-Docking

    Directory of Open Access Journals (Sweden)

    Zhi-Hua Hu

    2013-01-01

    Full Text Available Cross-docking, as a strategy to reduce lead time and enhance the efficiency of the fashion supply chain, has attracted substantial attention from both the academy and the industry. Cross-docking is a critical part of many fashion and textiles supply chains in practice because it can help to achieve many supply chain strategies such as postponement. We consider a model where there are multiple suppliers and customers in a single cross-docking center. With such a model setting, the issue concerning the coordinated routing between the inbound and outbound routes is much more complex than many traditional vehicle routing problems (VRPs. We formulate the optimal route selection problems from the suppliers to the cross-docking center and from the cross-docking center to the customers as the respective VRPs. Based on the relationships between the suppliers and the customers, we integrate the two VRP models to optimize the overall traveling time, distance, and waiting time at the cross-docking center. In addition, we propose a novel mixed 0/1 integer linear programming model by which the complexity of the problem can be reduced significantly. As demonstrated by the simulation analysis, our proposed model can be solved very efficiently by a commonly used optimization software package.

  14. The Asteroid Redirect Mission (ARM)

    Science.gov (United States)

    Abell, Paul; Gates, Michele; Johnson, Lindley; Chodas, Paul; Mazanek, Dan; Reeves, David; Ticker, Ronald

    2016-07-01

    To achieve its long-term goal of sending humans to Mars, the National Aeronautics and Space Administration (NASA) plans to proceed in a series of incrementally more complex human spaceflight missions. Today, human flight experience extends only to Low-Earth Orbit (LEO), and should problems arise during a mission, the crew can return to Earth in a matter of minutes to hours. The next logical step for human spaceflight is to gain flight experience in the vicinity of the Moon. These cis-lunar missions provide a "proving ground" for the testing of systems and operations while still accommodating an emergency return path to the Earth that would last only several days. Cis-lunar mission experience will be essential for more ambitious human missions beyond the Earth-Moon system, which will require weeks, months, or even years of transit time. In addition, NASA has been given a Grand Challenge to find all asteroid threats to human populations and know what to do about them. Obtaining knowledge of asteroid physical properties combined with performing technology demonstrations for planetary defense provide much needed information to address the issue of future asteroid impacts on Earth. Hence the combined objectives of human exploration and planetary defense give a rationale for the Asteroid Re-direct Mission (ARM). Mission Description: NASA's ARM consists of two mission segments: 1) the Asteroid Redirect Robotic Mission (ARRM), the first robotic mission to visit a large (greater than ~100 m diameter) near-Earth asteroid (NEA), collect a multi-ton boulder from its surface along with regolith samples, demonstrate a planetary defense technique, and return the asteroidal material to a stable orbit around the Moon; and 2) the Asteroid Redirect Crewed Mission (ARCM), in which astronauts will take the Orion capsule to rendezvous and dock with the robotic vehicle, conduct multiple extravehicular activities to explore the boulder, and return to Earth with samples. NASA's proposed

  15. Computational methods for molecular docking

    Energy Technology Data Exchange (ETDEWEB)

    Klebe, G. [BASF AG, Ludwigshafen (Germany); Lengauer, T.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.

  16. Reduction of N-Cyanomethyl Groups on a Macrocyclic Nickel(II) Complex Using Sodium Borohydride: Synthesis of a Complex Bearing Two N-(2-Aminoethyl) Pendant Arms

    International Nuclear Information System (INIS)

    The stepwise protonation constants for [NiL2]2+ were determined by a spectrophotometric titration.17 The approximate pKa1 value (ca. 3.6) was found to be somewhat larger than the pKa2 value (ca. 2.4), as usual. The low pKa1 and pKa2 values may be result from the relatively strong interactions between the functional groups and the central metal of the complex. NaBH4 is an efficient reagent for the reduction of [NiL1]2+ in the presence of methanol, even though the N-CH2CN groups are not involved in coordination. The stepwise protonation constants for [NiL2]2+ indicate that the pendant amino groups-central metal interactions are relatively strong

  17. Laser docking sensor engineering model

    Science.gov (United States)

    Dekome, Kent; Barr, Joseph M.

    1991-01-01

    NASA JSC has been involved in the development of Laser sensors for the past ten years in order to support future rendezvous and docking missions, both manned and unmanned. Although many candidate technologies have been breadboarded and evaluated, no sensor hardware designed specifically for rendezvous and docking applications has been demonstrated on-orbit. It has become apparent that representative sensors need to be flown and demonstrated as soon as possible, with minimal cost, to provide the capability of the technology in meeting NASA's future AR&C applications. Technology and commercial component reliability have progressed to where it is now feasible to fly hardware as a detailed test objective minimizing the overall cost and development time. This presentation will discuss the ongoing effort to convert an existing in-house developed breadboard to an engineering model configuration suitable for flight. The modifications include improving the ranger resolution and stability with an in-house design, replacing the rack mounted galvanometric scanner drivers with STD-bus cards, replacing the system controlling personal computer with a microcontroller, and repackaging the subsystems as appropriate. The sensor will use the performance parameters defined in previous JSC requirements working groups as design goals and be built to withstand the space environment where fiscally feasible. Testing of the in-house ranger design is expected to be completed in October. The results will be included in the presentation. Preliminary testing of the ranging circuitry indicates a range resolution of 4mm is possible. The sensor will be mounted in the payload bay on a shelf bracket and have command, control, and display capabilities using the payload general support computer via an RS422 data line.

  18. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

    OpenAIRE

    Romina Oliva; Edrisse Chermak; Luigi Cavallo

    2015-01-01

    In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a ...

  19. Dynamic/control interactions between flexible orbiting space-robot during grasping, docking and post-docking manoeuvres

    Science.gov (United States)

    Gasbarri, Paolo; Pisculli, Andrea

    2015-05-01

    Robotic systems are expected to play an increasingly important role in future space activities, such as repairing, upgrading, refuelling, and re-orbiting spacecraft. These technologies could potentially extend the life of satellites, enhance the capability of space systems, reduce the operation costs, and clean up the increasing space debris. Recent proposals for missions involving the use of space manipulators and/or automated transfer vehicles are presented as a solution for a lot of problems, which now affect the procedures and the performance of the in-orbit space systems. Other projects involving space manipulators have been developed by DARPA aiming to demonstrate several satellite servicing operations and technologies including rendez-vous, proximity operations and station-keeping, capture, docking, fluid transfer (specifically, "hydrazine"), and Orbit Replaceable Unit (ORU) transfer. Of course the dynamic coupling between the manipulator and its base mounting flexible solar arrays is very difficult to model. Furthermore, the motion planning of space robots is usually much more complicated than the motion planning of fixed-base manipulators. In this paper first of all the authors present a mixed NE/EL formulation suitable for synthesizing optimal control strategies during the deploying manoeuvres of robotic arms mounted on flexible orbiting platform (i.e. the chaser). Then two new control strategies able to compensate the flexibility excitations of the chaser satellite solar panels during the capturing of a flexible target spacecraft with the use of two robotic arms are presented and applied to a grasping manoeuvre. The mission is here divided into three main phases: the approaching, the docking and the post-grasping phase. Several numerical examples will complete the work.

  20. WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand-Receptor Docking.

    Science.gov (United States)

    Murphy, Robert B; Repasky, Matthew P; Greenwood, Jeremy R; Tubert-Brohman, Ivan; Jerome, Steven; Annabhimoju, Ramakrishna; Boyles, Nicholas A; Schmitz, Christopher D; Abel, Robert; Farid, Ramy; Friesner, Richard A

    2016-05-12

    We have developed a new methodology for protein-ligand docking and scoring, WScore, incorporating a flexible description of explicit water molecules. The locations and thermodynamics of the waters are derived from a WaterMap molecular dynamics simulation. The water structure is employed to provide an atomic level description of ligand and protein desolvation. WScore also contains a detailed model for localized ligand and protein strain energy and integrates an MM-GBSA scoring component with these terms to assess delocalized strain of the complex. Ensemble docking is used to take into account induced fit effects on the receptor conformation, and protein reorganization free energies are assigned via fitting to experimental data. The performance of the method is evaluated for pose prediction, rank ordering of self-docked complexes, and enrichment in virtual screening, using a large data set of PDB complexes and compared with the Glide SP and Glide XP models; significant improvements are obtained. PMID:27054459

  1. Design of an I-Shaped Less-Than-Truckload Cross-Dock: A Simulation Experiment Study

    Science.gov (United States)

    Leng, Kaijun; Shi, Wen; Chen, Jinbo; Lv, Zhihan

    2015-12-01

    The most important decision in cross-docking design is the number of unloading and loading doors. This paper focuses on the design issues of unloading and loading doors of symmetric-I-shaped (I-LTL) cross-docks pervasive in the Chinese auto-part supplying chain which is obviously a very complex system. First of all, this paper analyzes the operation process of I-LTL cross-docking in detail and completes the construction of discrete event simulation that conforms to I-LTL cross-docking operation on the basis of practical details in reality through ARENA platform. In the simulation analysis, this paper selects the physical flow of parts (supporting for arrival frequency and loading capacity of transport vehicles) and I-LTL cross-docking as the simulation experimental factors and applies multilevel factorial design to carry out a large-scale simulation experiment. The results suggest that the required number of receiving dock doors is determined by the arrival frequency of storage vehicles and loading capacity. Moreover, the effect of arrival frequency index is far greater than the loading capacity index. On the other hand, the required number of shipping dock doors primarily depends on the cross-docking consolidation rate and vehicle arrival frequency. Moreover, the index action of consolidation rate is greater than the effect of arriving frequency linearity.

  2. Development of a Robotics-based Satellites Docking Simulator

    NARCIS (Netherlands)

    Zebenay, M.

    2014-01-01

    The European Proximity Operation Simulator (EPOS) is a hardware-in-the-loop (HIL) system aiming, among other objectives, at emulating on-orbit docking of spacecraft for verification and validation of the docking phase. This HIL docking simulator set-up essentially consists of docking interfaces, sim

  3. Docking and scoring of metallo-beta-lactamases inhibitors

    DEFF Research Database (Denmark)

    Olsen, Lars; Pettersson, Ingrid; Hemmingsen, Lars; Adolph, Hans-Werner; Jørgensen, Flemming Steen

    2004-01-01

    The performance of the AutoDock, GOLD and FlexX docking programs was evaluated for docking of dicarboxylic acid inhibitors into metallo-beta-lactamases (MBLs). GOLD provided the best overall performance, with RMSDs between experimental and docked structures of 1.8-2.6 A and a good correlation bet...

  4. Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

    Directory of Open Access Journals (Sweden)

    Tyagi Sadhna

    2009-06-01

    Full Text Available Abstract Background Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions. Results Here we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate complex. After a second round of docking the same substrate into the geometry-optimised structures, productive poses are identified by geometric filter criteria and ranked by their docking scores. Substrate-imprinted docking was applied in order to model (i enantioselectivity of Candida antarctica lipase B and a W104A mutant, (ii enantioselectivity and substrate specificity of Candida rugosa lipase and Burkholderia cepacia lipase, and (iii substrate specificity of an acetyl- and a butyrylcholine esterase toward the substrates acetyl- and butyrylcholine. Conclusion The experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand, although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria.

  5. Histopathological Characterization of Tail Injury and Traumatic Neuroma Development after Tail Docking in Piglets.

    Science.gov (United States)

    Sandercock, D A; Smith, S H; Di Giminiani, P; Edwards, S A

    2016-07-01

    Tail docking of neonatal pigs is widely used as a measure to reduce the incidence of tail biting, a complex management problem in the pig industry. Concerns exist over the long-term consequences of tail docking for possible tail stump pain sensitivity due to the development of traumatic neuromas in injured peripheral nerves. Tail stumps were obtained post mortem from four female pigs at each of 1, 4, 8 and 16 weeks following tail amputation (approximately two-thirds removed) by a gas-heated docking iron on post natal day 3. Tissues were processed routinely for histopathological examination. Non-neural inflammatory and reparative epidermal and dermal changes associated with tissue thickening and healing were observed 1 to 4 months after docking. Mild neutrophilic inflammation was present in some cases, although this and other degenerative and non-neural reparative changes are not likely to have caused pain. Traumatic neuroma and neuromatous tissue development was not observed 1 week after tail docking, but was evident 1 month after tail docking. Over time there was marked nerve sheath and axonal proliferation leading to the formation of neuromata, which were either localized and circumscribed or comprised of multiple axons dispersed within granulation tissue. Four months after tail resection, neuroma formation was still incomplete, with possible implications for sensitivity of the tail stump. PMID:27302763

  6. A Review on Quantitative Approaches for Dock Door Assignment in Cross-Docking

    OpenAIRE

    Adibah Shuib; Wan Nor Ashikin Wan Ahmad Fatthi

    2012-01-01

    Cross docking is a relatively new technique in supply chain operations. It offers limited storage time to maximize the efficiency of goods transshipment. Efficient operation of a cross docking system requires an appropriate coordination of inbound and outbound flows, accurate planning and dynamic scheduling.  The planning strategies at cross docking terminals, which are receiving growing attention today, are the truck-to-door assignment and destination to door assignment problems. This paper ...

  7. Ranking multiple docking solutions based on the conservation of inter-residue contacts

    KAUST Repository

    Oliva, Romina M.

    2013-06-17

    Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.

  8. A COMPLEX ADAPTIVE STATE SYSTEM: NETWORKS, ARMS RACES AND MORAL HAZARDS Un sistema adaptativo complejo: Redes, carreras armamentistas y peligros morales

    Directory of Open Access Journals (Sweden)

    PABLO POLICZER

    2012-01-01

    Full Text Available Much of the debate over stateness in Latin America assumes that states should sustain basic levels of stability, and if they cannot, the question is why not. This article departs from the assumption of stability, by asking how the relationship between states and other actors has evolved over time. This departure requires a shift in focus: from stateness as referring to states and how they should operate, to stateness as referring to the relationships between states and other actors, and how they change over time. The article argues that such relationships can be understood as emergent complex adaptive systems (CAS, and considers three specific CAS mechanisms: networks, arms races, and moral hazards. This conceptual shift in how to think about states is especially challenging in a region historically accustomed to hierarchical governance.Buena parte del debate sobre la estatalidad en América Latina presupone que los estados deben mantener niveles básicos de estabilidad, y que si no pueden hacerlo, la pregunta es por qué no. Este artículo se aleja del supuesto de la estabilidad, al preguntar cómo la relación entre los estados y otros actores ha evolucionado con el tiempo. Esto requiere un cambio de enfoque: de estatalidad que se refiere a los estados y cómo debieran funcionar, a la estatalidad en referencia a las relaciones entre los estados y otros actores, y cómo éstas cambian con el tiempo. El artículo sostiene que este tipo de relaciones se puede entender como sistemas complejos adaptativos (SCA emergentes, y considera tres mecanismos específicos de SCA: redes, carreras armamentistas y peligros morales (moral hazards. Este cambio conceptual en laforma de pensar acerca de los estados es especialmente difícil en una región históricamente acostumbrada a la gobernanza jerárquica.

  9. Cyclam kappa4 to kappa3 ligand denticity change upon mono-n-substitution with a carboxypropyl pendant arm in a ruthenium nitrosyl complex.

    Science.gov (United States)

    Doro, Fábio G; Castellano, Eduardo E; Moraes, Luiz A B; Eberlin, Marcos N; Tfouni, Elia

    2008-05-19

    The complex fac-[Ru(NO)Cl2(kappa(3)N(4),N(8),N(11)(1-carboxypropyl)cyclam)]Cl.H2O (1-carboxypropyl)cyclam=3-(1,4,8,11-tetraazacyclotetradecan-1-yl)propionic acid) was prepared in a one pot reaction by mixing equimolar amounts of RuNOCl 3 and (1-carboxypropyl)cyclam and was characterized by X-ray crystallography, electrospray ionization tandem mass spectrometry (ESI-MS/MS), elemental analysis, NMR, and electronic and vibrational (IR) spectroscopies. fac-[Ru(NO)Cl 2(kappa(3)N(4),N(8),N(11)(1-carboxypropyl)cyclam)]Cl.H2O crystallizes in the triclinic, space group P1, No. 2, with unit cell parameters of a=8.501(1) A, b=9.157(1) A, c=14.200(1) A, alpha=72.564(5) degrees , beta=82.512(5) degrees , gamma=80.308(5) degrees , and Z=2. The Ru-N interatomic distance and bond angle in the [Ru-NO] unit are 1.739(2) A and 167.7(2) degrees , respectively. ESI-MS/MS shows characteristic dissociation chemistry that initiates by HCl or NO loss. The IR spectrum displays a nu(NO) at 1881 cm(-1) indicating a nitrosonium character. The electronic spectrum shows absorptions bands at 264 nm (log epsilon=3.27), 404 nm (log epsilon=2.53), and 532 nm (log epsilon=1.88). (1)H and (13)C NMR are in agreement with the proposed molecular structure, which shows a very singular architecture where the cyclam ring N (with the carboxypropyl pendant arm) is not coordinated to the ruthenium resulting in a kappa(3) instead of the expected kappa(4) denticity. PMID:18399626

  10. Use of the docking dynamics test facility for rendezvous and docking final approach verification

    Science.gov (United States)

    Noirault, P.; Pairot, J. M.

    1991-12-01

    The Docking and Dynamics Test Facility (DDTF) and its current areas of investigation are reviewed. The following topics are described: tests of an automatic scenario with a closed loop control of the approach to docking using a RV (Rendezvous) sensor breadboard; tests with a representative mockup of the future Docking/Berthing System (DBS), to derive relevant allocation between the GNC (Guidance, Navigation, and Control) system performances and the DBS capabilities; and tests on the last 5 m translation with full human control of the chaser for the Hermes/Columbus mission, where astronauts performed the docking mission. Some recommendations for a future dynamical test bench are given in conclusion.

  11. Rapid flexible docking using a stochastic rotamer library of ligands

    OpenAIRE

    Ding, Feng; Yin, Shuangye; Dokholyan, Nikolay V.

    2010-01-01

    Existing flexible docking approaches model the ligand and receptor flexibility either separately or in a loosely-coupled manner, which captures the conformational changes inefficiently. Here, we propose a flexible docking approach, MedusaDock, which models both ligand and receptor flexibility simultaneously with sets of discrete rotamers. We develop an algorithm to build the ligand rotamer library “on-the-fly” during docking simulations. MedusaDock benchmarks demonstrate a rapid sampling effi...

  12. Structural basis for mutual relief of the Rac guanine nucleotide exchange factor DOCK2 and its partner ELMO1 from their autoinhibited forms

    OpenAIRE

    Hanawa-Suetsugu, Kyoko; Kukimoto-Niino, Mutsuko; Mishima-Tsumagari, Chiemi; Akasaka, Ryogo; Ohsawa, Noboru; Sekine, Shun-ichi; Ito, Takuhiro; Tochio, Naoya; Koshiba, Seizo; Kigawa, Takanori; Terada, Takaho; Shirouzu, Mikako; Nishikimi, Akihiko; Uruno, Takehito; Katakai, Tomoya

    2012-01-01

    DOCK2, a hematopoietic cell-specific, atypical guanine nucleotide exchange factor, controls lymphocyte migration through ras-related C3 botulinum toxin substrate (Rac) activation. Dedicator of cytokinesis 2–engulfment and cell motility protein 1 (DOCK2•ELMO1) complex formation is required for DOCK2-mediated Rac signaling. In this study, we identified the N-terminal 177-residue fragment and the C-terminal 196-residue fragment of human DOCK2 and ELMO1, respectively, as the mutual binding region...

  13. The RhoG/ELMO1/Dock180 signaling module is required for spine morphogenesis in hippocampal neurons.

    Science.gov (United States)

    Kim, Jeong-Yoon; Oh, Mi Hee; Bernard, Laura P; Macara, Ian G; Zhang, Huaye

    2011-10-28

    Dendritic spines are actin-rich structures, the formation and plasticity of which are regulated by the Rho GTPases in response to synaptic input. Although several guanine nucleotide exchange factors (GEFs) have been implicated in spine development and plasticity in hippocampal neurons, it is not known how many different Rho GEFs contribute to spine morphogenesis or how they coordinate the initiation, establishment, and maintenance of spines. In this study, we screened 70 rat Rho GEFs in cultured hippocampal neurons by RNA interference and identified a number of candidates that affected spine morphogenesis. Of these, Dock180, which plays a pivotal role in a variety of cellular processes including cell migration and phagocytosis, was further investigated. We show that depletion of Dock180 inhibits spine morphogenesis, whereas overexpression of Dock180 promotes spine morphogenesis. ELMO1, a protein necessary for in vivo functions of Dock180, functions in a complex with Dock180 in spine morphogenesis through activating the Rac GTPase. Moreover, RhoG, which functions upstream of the ELMO1/Dock180 complex, is also important for spine formation. Together, our findings uncover a role for the RhoG/ELMO1/Dock180 signaling module in spine morphogenesis in hippocampal neurons. PMID:21900250

  14. An alpha-helical extension of the ELMO1 pleckstrin homology domain mediates direct interaction to DOCK180 and is critical in Rac signaling.

    Science.gov (United States)

    Komander, David; Patel, Manishha; Laurin, Mélanie; Fradet, Nadine; Pelletier, Ariane; Barford, David; Côté, Jean-François

    2008-11-01

    The mammalian DOCK180 protein belongs to an evolutionarily conserved protein family, which together with ELMO proteins, is essential for activation of Rac GTPase-dependent biological processes. Here, we have analyzed the DOCK180-ELMO1 interaction, and map direct interaction interfaces to the N-terminal 200 amino acids of DOCK180, and to the C-terminal 200 amino acids of ELMO1, comprising the ELMO1 PH domain. Structural and biochemical analysis of this PH domain reveals that it is incapable of phospholipid binding, but instead structurally resembles FERM domains. Moreover, the structure revealed an N-terminal amphiphatic alpha-helix, and point mutants of invariant hydrophobic residues in this helix disrupt ELMO1-DOCK180 complex formation. A secondary interaction between ELMO1 and DOCK180 is conferred by the DOCK180 SH3 domain and proline-rich motifs at the ELMO1 C-terminus. Mutation of both DOCK180-interaction sites on ELMO1 is required to disrupt the DOCK180-ELMO1 complex. Significantly, although this does not affect DOCK180 GEF activity toward Rac in vivo, Rac signaling is impaired, implying additional roles for ELMO in mediating intracellular Rac signaling. PMID:18768751

  15. Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

    Science.gov (United States)

    Brylinski, Michal

    2013-11-25

    A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely

  16. Spectroscopic investigations of Eu{sup 3+}-complexes with ligands containing multiple diglycolamide pendant arms in a room temperature ionic liquid

    Energy Technology Data Exchange (ETDEWEB)

    Sengupta, Arijit [Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India); Mohapatra, Prasanta K., E-mail: mpatra@barc.gov.in [Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085 (India); Iqbal, Mudassir; Huskens, Jurriaan; Verboom, Willem [Laboratory of Molecular Nanofabrication, MESA" + Institute for Nanotechnology, University of Twente, P. O. Box 217, 7500 AE Enschede (Netherlands)

    2014-10-15

    Fluorescence spectroscopy was used to study the complexation of different ligands containing multiple diglycolamide (DGA) pendent arms such as T-DGA (tripodal diglycolamide), C4DGA (upper rim functionalized calix [4] arene with four DGA moieties), and C8DGA (both side functionalized calix [4] arene with eight DGA moieties) with Eu{sup 3+} in ionic liquids such as C{sub 4}mimNTf{sub 2} and C{sub 8}mimNTf{sub 2} (1-alkyl-3-methylimidazolium bis(trifluoromethylsulphonyl)imide). Mainly five sets of emission profiles were observed in all the spectra (1st set at∼580 nm assigned as the {sup 5}D{sub 0}→{sup 7}F{sub 0} transition, 2nd set at∼593 nm assigned as the {sup 5}D{sub 0}→{sup 7}F{sub 1} transition, 3rd set at∼613 nm assigned as the {sup 5}D{sub 0}→{sup 7}F{sub 2} transition, 4th set at∼650 nm assigned as the {sup 5}D{sub 0}→{sup 7}F{sub 3} transition, and 5th set at∼700 nm assigned as the {sup 5}D{sub 0}→{sup 7}F{sub 4} transition). The difference in the spectral features revealed that the nature of the complexes differs significantly from one another. Judd–Offelt constant Ω{sub 2}, which is a measure of the covalency of the metal–ligand bond, follows the order Eu{sup 3+}–C4DGA (C{sub 8}mimNTf{sub 2})>Eu{sup 3+}–C8DGA (C{sub 8}mimNTf{sub 2})>Eu{sup 3+}–TODGA (C{sub 4}mimNTf{sub 2})>Eu{sup 3+}–T-DGA (C{sub 4}mimNTf{sub 2})>Eu{sup 3+}{sub aq}. The high intensity of the {sup 5}D{sub 0}→{sup 7}F{sub 2} transitions in all complexes suggests that Eu{sup 3+} resides in a highly asymmetric environment. From the splitting patterns of the transitions, the local site symmetry around Eu{sup 3+} was found to be C{sub 2V} for the Eu{sup 3+}–T-DGA complex in both C{sub 4}mimNTf{sub 2} and a 1:5 acetonitrile–water mixture, C{sub 4V} for Eu{sup 3+}–C8DGA and Eu{sup 3+}–TODGA complexes, and either C{sub 1}, C{sub 2}, or C{sub S} for the Eu{sup 3+}–C4DGA complex. A linear relationship between the {sup 5}D{sub 0}–{sup 7}F{sub 1} splitting

  17. Tail docking in pigs: acute physiological and behavioural responses.

    Science.gov (United States)

    Sutherland, M A; Bryer, P J; Krebs, N; McGlone, J J

    2008-02-01

    Tail docking of piglets is a routine procedure on farms to control tail-biting behaviour; however, docking can cause an acute stress response. The objectives of this research were to determine the stress responses to tail docking in piglets and to compare two methods of tail docking; cautery iron (CAUT) and the more commonly used blunt trauma cutters (BT). At approximately 6 days of age, piglets were tail docked using CAUT (n = 20), BT (n = 20) or sham tail docked with their tails remaining intact (CON; n = 40). Blood samples were taken prior to tail docking and at 30, 60 and 90 min after tail docking to evaluate the effect of tail docking on white blood cell (WBC) measures and cortisol concentrations. The above experiment was repeated to observe behaviour without the periodic blood sampling, so as not to confound the effects of blood sampling on piglet behaviour. Piglet behaviour was recorded in the farrowing crate using 1 min scan-samples via live observations for 60 min prior to and 90 min after tail docking. Total WBC counts were reduced (P > 0.05) among BT and CAUT compared with CON piglets 30 min after tail docking. Cortisol concentrations were higher (P tail docking. Cautery and BT-docked piglets spent more (P tail docking. Piglets tail docked using CAUT and BT tended to spend more (P tail docking. Elevated blood cortisol can be reduced by the use of the CAUT rather than the BT method of tail docking. Although the tail docking-induced rise in cortisol was prevented by using CAUT, the behavioural response to BT and CAUT docking methods was similar. PMID:22445023

  18. Introduction to Reading and Visualizing ARM Data

    Energy Technology Data Exchange (ETDEWEB)

    Mather, James [Pacific Northwest National Laboratory

    2014-02-18

    Atmospheric Radiation Measurement (ARM) Program standard data format is NetCDF 3 (Network Common Data Form). The object of this tutorial is to provide a basic introduction to NetCDF with an emphasis on aspects of the ARM application of NetCDF. The goal is to provide basic instructions for reading and visualizing ARM NetCDF data with the expectation that these examples can then be applied to more complex applications.

  19. An Insight into the Anticancer Activities of Ru(II-Based Metallocompounds Using Docking Methods

    Directory of Open Access Journals (Sweden)

    Peter A. Ajibade

    2013-09-01

    Full Text Available Unlike organic molecules, reports on docking of metal complexes are very few; mainly due to the inadequacy of force fields in docking packages to appropriately characterize the metal atoms that consequentially hinder the rational design of metal-based drug complexes. In this study we have made used Molegro and Autodock to predict the anticancer activities of selected Ru(II complexes against twelve anticancer targets. We observed that introducing the quantum calculated atomic charges of the optimized geometries significantly improved the docking predictions of these anticancer metallocompounds. Despite several limitations in the docking of metal-based complexes, we obtained results that are highly correlated with the available experimental results. Most of our newly proposed metallocompounds are found theoretically to be better anticancer metallocompounds than all the experimentally proposed RAPTA complexes. An interesting features of a strong interactions of new modeled of metallocompounds against the two base edges of DNA strands suggest similar mechanisms of anticancer activities similar to that of cisplatin. There is possibility of covalent bonding between the metal center of the metallocompounds and the residues of the receptors DNA-1, DNA-2, HDAC7, HIS and RNR. However, the general results suggest the possibility of metals positioning the coordinated ligands in the right position for optimal receptor interactions and synergistic effects, rather than forming covalent bonds.

  20. Quantum mechanical/molecular mechanical (QM/MM) docking: an evaluation for known test systems

    Science.gov (United States)

    Beierlein, Frank; Lanig, Harald; Schürer, Gudrun; Horn, Anselm H. C.; Clark, Timothy

    A combined quantum mechanical/molecular mechanical (QM/MM) docking approach for the investigation of protein-inhibitor complexes is presented. Starting points for QM/MM optimizations are generated with AutoDock. The subsequent semiempirical AM1 QM/MM optimization of the complex obtained by the docking procedure gives a more detailed description of the binding mode and the electronic properties of the ligand. As we use a flexible protein environment in the QM/MM optimizations, we are able to simulate limited structural changes of the enzyme upon binding a ligand, even within a simple geometry optimization. The method was validated using a set of structurally known protein-inhibitor complexes, whose crystallographic data were taken from the Protein Data Bank. In addition to protein structures taken directly from complexes with the inhibitors, structures of uncomplexed HIV-1-protease and thrombin were also used successfully for QM/MM docking experiments. By comparing the resulting structures with those obtained using protein structures from protein-inhibitor complexes, we find that the method is able to simulate the effect of the induced fit when a simple optimization is adequate to reproduce the protein movement. Describing the ligand quantum mechanically gives a detailed view of its electronic properties, for example its polarization within the active site of the enzyme. This study suggests strongly that a QM/MM molecular dynamics approach will be able to simulate the induced fit in general cases.

  1. Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking.

    Science.gov (United States)

    Nivedha, Anita K; Thieker, David F; Makeneni, Spandana; Hu, Huimin; Woods, Robert J

    2016-02-01

    Molecular docking programs are primarily designed to align rigid, drug-like fragments into the binding sites of macromolecules and frequently display poor performance when applied to flexible carbohydrate molecules. A critical source of flexibility within an oligosaccharide is the glycosidic linkages. Recently, Carbohydrate Intrinsic (CHI) energy functions were reported that attempt to quantify the glycosidic torsion angle preferences. In the present work, the CHI-energy functions have been incorporated into the AutoDock Vina (ADV) scoring function, subsequently termed Vina-Carb (VC). Two user-adjustable parameters have been introduced, namely, a CHI- energy weight term (chi_coeff) that affects the magnitude of the CHI-energy penalty and a CHI-cutoff term (chi_cutoff) that negates CHI-energy penalties below a specified value. A data set consisting of 101 protein-carbohydrate complexes and 29 apoprotein structures was used in the development and testing of VC, including antibodies, lectins, and carbohydrate binding modules. Accounting for the intramolecular energies of the glycosidic linkages in the oligosaccharides during docking led VC to produce acceptable structures within the top five ranked poses in 74% of the systems tested, compared to a success rate of 55% for ADV. An enzyme system was employed in order to illustrate the potential application of VC to proteins that may distort glycosidic linkages of carbohydrate ligands upon binding. VC represents a significant step toward accurately predicting the structures of protein-carbohydrate complexes. Furthermore, the described approach is conceptually applicable to any class of ligands that populate well-defined conformational states. PMID:26744922

  2. Pharmacophore modeling, 3D-QSAR and docking study of 2-phenylpyrimidine analogues as selective PDE4B inhibitors.

    Science.gov (United States)

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2016-04-01

    Pharmacophore modeling, molecular docking, and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 2-phenylpyrimidine series as PDE4B selective inhibitors. A five point pharmacophore model was developed using 87 molecules having pIC50 ranging from 8.52 to 5.07. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2)=0.918), cross validation coefficient (Q(2)=0.852), and F value (175) at 4 component PLS factor. The external validation indicated that our QSAR model possessed high predictive power (R(2)=0.70). The generated model was further validated by enrichment studies using the decoy test. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviation. A 10ns molecular dynamics simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Further, similar orientation was observed between the superposition of the conformations of 85 after MD simulation and best XP-docking pose; MD simulation and 3D-QSAR pose; best XP-docking and 3D-QSAR poses. Outcomes of the present study provide insight in designing novel molecules with better PDE4B selective inhibitory activity. PMID:26804643

  3. MAGIC: Marine ARM GPCI Investigation of Clouds

    Energy Technology Data Exchange (ETDEWEB)

    Lewis, ER; Wiscombe, WJ; Albrecht, BA; Bland, GL; Flagg, CN; Klein, SA; Kollias, P; Mace, G; Reynolds, RM; Schwartz, SE; Siebesma, AP; Teixeira, J; Wood, R; Zhang, M

    2012-10-03

    The second Atmospheric Radiation Measurement (ARM) Mobile Facility (AMF2) will be deployed aboard the Horizon Lines cargo container ship merchant vessel (M/V) Spirit for MAGIC, the Marine ARM GPCI1 Investigation of Clouds. The Spirit will traverse the route between Los Angeles, California, and Honolulu, Hawaii, from October 2012 through September 2013 (except for a few months in the middle of this time period when the ship will be in dry dock). During this field campaign, AMF2 will observe and characterize the properties of clouds and precipitation, aerosols, and atmospheric radiation; standard meteorological and oceanographic variables; and atmospheric structure. There will also be two intensive observational periods (IOPs), one in January 2013 and one in July 2013, during which more detailed measurements of the atmospheric structure will be made.

  4. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment

    DEFF Research Database (Denmark)

    Kufareva, Irina; Katritch, Vsevolod; Biggin, Phil;

    2014-01-01

    Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock asse...

  5. Histopathological Characterization of Tail Injury and Traumatic Neuroma Development after Tail Docking in Piglets

    OpenAIRE

    Sandercock, D A; Smith, S H; Di Giminiani, P.; Edwards, S. A.

    2016-01-01

    Tail docking of neonatal pigs is widely used as a measure to reduce the incidence of tail biting, a complex management problem in the pig industry. Concerns exist over the long-term consequences of tail docking for possible tail stump pain sensitivity due to the development of traumatic neuromas in injured peripheral nerves. Tail stumps were obtained post mortem from four female pigs at each of 1, 4, 8 and 16 weeks following tail amputation (approximately two-thirds removed) by a gas-heated d...

  6. A computational system for modelling flexible protein-protein and protein-DNA docking.

    Science.gov (United States)

    Sternberg, M J; Aloy, P; Gabb, H A; Jackson, R M; Moont, G; Querol, E; Aviles, F X

    1998-01-01

    A computational system is described that predicts the structure of protein/protein and protein/DNA complexes starting from unbound coordinate sets. The approach is (i) a global search with rigid-body docking for complexes with shape complementarity and favourable electrostatics; (ii) use of distance constraints from experimental (or predicted) knowledge of critical residues; (iii) use of pair potential to screen docked complexes and (iv) refinement and further screening by protein-side chain optimisation and interfacial energy minimisation. The system has been applied to model ten protein/protein and eight protein-repressor/DNA (steps i to iii only) complexes. In general a few complexes, one of which is close to the true structure, can be generated. PMID:9783224

  7. Using RosettaLigand for small molecule docking into comparative models.

    Directory of Open Access Journals (Sweden)

    Kristian W Kaufmann

    Full Text Available Computational small molecule docking into comparative models of proteins is widely used to query protein function and in the development of small molecule therapeutics. We benchmark RosettaLigand docking into comparative models for nine proteins built during CASP8 that contain ligands. We supplement the study with 21 additional protein/ligand complexes to cover a wider space of chemotypes. During a full docking run in 21 of the 30 cases, RosettaLigand successfully found a native-like binding mode among the top ten scoring binding modes. From the benchmark cases we find that careful template selection based on ligand occupancy provides the best chance of success while overall sequence identity between template and target do not appear to improve results. We also find that binding energy normalized by atom number is often less than -0.4 in native-like binding modes.

  8. DockQ: A Quality Measure for Protein-Protein Docking Models.

    Science.gov (United States)

    Basu, Sankar; Wallner, Björn

    2016-01-01

    The state-of-the-art to assess the structural quality of docking models is currently based on three related yet independent quality measures: Fnat, LRMS, and iRMS as proposed and standardized by CAPRI. These quality measures quantify different aspects of the quality of a particular docking model and need to be viewed together to reveal the true quality, e.g. a model with relatively poor LRMS (>10Å) might still qualify as 'acceptable' with a descent Fnat (>0.50) and iRMS (github.com/bjornwallner/DockQ/. PMID:27560519

  9. SwarmDock and the Use of Normal Modes in Protein-Protein Docking

    Directory of Open Access Journals (Sweden)

    Paul A. Bates

    2010-09-01

    Full Text Available Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.

  10. CALET docked on the ISS

    CERN Multimedia

    Antonella Del Rosso

    2015-01-01

    On 19 August, with a spectacular launch on board the Japanese H2-B rocket operated by the Japan Aerospace Exploration Agency (JAXA), the CALorimetric Electron Telescope (CALET) left the Tanegashima Space Center to reach the International Space Station five days later.   After berthing with the ISS, CALET was extracted by a robotic arm from the Japanese HTV-5 transfer vehicle and installed on the Japanese Exposure Facility (right) where it will start its first data-taking. (Image: NASA/JAXA.)   CALET is a space mission led by JAXA with the participation of the Italian Space Agency (ASI) and NASA. It is a CERN-recognised experiment and the second high-energy astroparticle experiment to be installed on the International Space Station (ISS) after AMS-02, which has been taking data since 2011. Designed to be a space observatory for long-term observations of cosmic radiation aboard the external platform JEM-EF of the Japanese module (KIBO) on the ISS, CALET aims to identify elect...

  11. Development of a Robotics-based Satellites Docking Simulator

    OpenAIRE

    Zebenay, M.

    2014-01-01

    The European Proximity Operation Simulator (EPOS) is a hardware-in-the-loop (HIL) system aiming, among other objectives, at emulating on-orbit docking of spacecraft for verification and validation of the docking phase. This HIL docking simulator set-up essentially consists of docking interfaces, simulating the servicing satellite called chaser satellite, the serviced satellite called target satellite, a sensor of the forces and torques during contact, and two industrial robots that hold the d...

  12. Solving molecular docking problems with multi-objective metaheuristics.

    Science.gov (United States)

    García-Godoy, María Jesús; López-Camacho, Esteban; García-Nieto, José; Aldana-Montes, Antonio J Nebroand José F

    2015-01-01

    Molecular docking is a hard optimization problem that has been tackled in the past with metaheuristics, demonstrating new and challenging results when looking for one objective: the minimum binding energy. However, only a few papers can be found in the literature that deal with this problem by means of a multi-objective approach, and no experimental comparisons have been made in order to clarify which of them has the best overall performance. In this paper, we use and compare, for the first time, a set of representative multi-objective optimization algorithms applied to solve complex molecular docking problems. The approach followed is focused on optimizing the intermolecular and intramolecular energies as two main objectives to minimize. Specifically, these algorithms are: two variants of the non-dominated sorting genetic algorithm II (NSGA-II), speed modulation multi-objective particle swarm optimization (SMPSO), third evolution step of generalized differential evolution (GDE3), multi-objective evolutionary algorithm based on decomposition (MOEA/D) and S-metric evolutionary multi-objective optimization (SMS-EMOA). We assess the performance of the algorithms by applying quality indicators intended to measure convergence and the diversity of the generated Pareto front approximations. We carry out a comparison with another reference mono-objective algorithm in the problem domain (Lamarckian genetic algorithm (LGA) provided by the AutoDock tool). Furthermore, the ligand binding site and molecular interactions of computed solutions are analyzed, showing promising results for the multi-objective approaches. In addition, a case study of application for aeroplysinin-1 is performed, showing the effectiveness of our multi-objective approach in drug discovery. PMID:26042856

  13. Solving Molecular Docking Problems with Multi-Objective Metaheuristics

    Directory of Open Access Journals (Sweden)

    María Jesús García-Godoy

    2015-06-01

    Full Text Available Molecular docking is a hard optimization problem that has been tackled in the past with metaheuristics, demonstrating new and challenging results when looking for one objective: the minimum binding energy. However, only a few papers can be found in the literature that deal with this problem by means of a multi-objective approach, and no experimental comparisons have been made in order to clarify which of them has the best overall performance. In this paper, we use and compare, for the first time, a set of representative multi-objective optimization algorithms applied to solve complex molecular docking problems. The approach followed is focused on optimizing the intermolecular and intramolecular energies as two main objectives to minimize. Specifically, these algorithms are: two variants of the non-dominated sorting genetic algorithm II (NSGA-II, speed modulation multi-objective particle swarm optimization (SMPSO, third evolution step of generalized differential evolution (GDE3, multi-objective evolutionary algorithm based on decomposition (MOEA/D and S-metric evolutionary multi-objective optimization (SMS-EMOA. We assess the performance of the algorithms by applying quality indicators intended to measure convergence and the diversity of the generated Pareto front approximations. We carry out a comparison with another reference mono-objective algorithm in the problem domain (Lamarckian genetic algorithm (LGA provided by the AutoDock tool. Furthermore, the ligand binding site and molecular interactions of computed solutions are analyzed, showing promising results for the multi-objective approaches. In addition, a case study of application for aeroplysinin-1 is performed, showing the effectiveness of our multi-objective approach in drug discovery.

  14. Cross Coupling Between Attenuators In A Docking Mechanism

    Science.gov (United States)

    Holmberg, Arthur; Schmidt, Matthew S.; Ghofranian, Siamak

    1996-01-01

    Cross coupling between motion attenuators on opposite sides of docking mechanism proposed as means of increasing capture envelope. Prototype system for application of cross-coupling concept is one used for docking of Apollo and Soyuz spacecraft; however, given widespread use of docking mechanisms, concept may prove useful in many terrestrial applications as well.

  15. Docking-mechanism attenuator with electromechanical damper

    Science.gov (United States)

    Syromyatnikov, V. S.

    1971-01-01

    Theoretical and practical problems involved in the application of electromechanical damping for spacecraft docking-mechanism attenuation are discussed. Some drawbacks of hydraulic dampers used for the purpose are pointed out. The basic scheme of the attenuator with the electromechanical damper is given.

  16. Operator learning effects in teleoperated rendezvous & docking

    Science.gov (United States)

    Wilde, M.; Harder, J.; Purschke, R.

    Teleoperation of spacecraft proximity operations and docking requires delicate timing and coordination of spacecraft maneuvers. Experience has shown that human operators show large performance fluctuations in these areas, which are a major factor to be addressed in operator training. In order to allow the quantification of the impact of these human fluctuations on control system performance and the human perception of this performance, a learning curve study was conducted with teleoperated final approach and docking scenarios. Over a period of ten experiment days, three test participants were tasked with repeatedly completing a set of three training scenarios. The scenarios were designed to contain different combinations of the major elements of any final approach and docking situation, and to feature an increasing difficulty level. The individual difficulty levels for the three operators furthermore differed in the level of operator support functions available in their human-machine interfaces. Operator performance in the test scenarios were evaluated in the fields approach success and precision, docking safety, and approach efficiency by a combination of recorded maneuver data and questionnaires. The results show that operator experience and the associated learning curves increase operator performance substantially, regardless of the support system used. The paper also shows that the fluctuations in operator performance and self-perception are substantial between as well as within experiment days, and must be reckoned with in teleoperation system design and mission planning.

  17. The Rac1 regulator ELMO controls basal body migration and docking in multiciliated cells through interaction with Ezrin.

    Science.gov (United States)

    Epting, Daniel; Slanchev, Krasimir; Boehlke, Christopher; Hoff, Sylvia; Loges, Niki T; Yasunaga, Takayuki; Indorf, Lara; Nestel, Sigrun; Lienkamp, Soeren S; Omran, Heymut; Kuehn, E Wolfgang; Ronneberger, Olaf; Walz, Gerd; Kramer-Zucker, Albrecht

    2015-01-01

    Cilia are microtubule-based organelles that are present on most cells and are required for normal tissue development and function. Defective cilia cause complex syndromes with multiple organ manifestations termed ciliopathies. A crucial step during ciliogenesis in multiciliated cells (MCCs) is the association of future basal bodies with the apical plasma membrane, followed by their correct spacing and planar orientation. Here, we report a novel role for ELMO-DOCK1, which is a bipartite guanine nucleotide exchange factor complex for the small GTPase Rac1, and for the membrane-cytoskeletal linker Ezrin, in regulating centriole/basal body migration, docking and spacing. Downregulation of each component results in ciliopathy-related phenotypes in zebrafish and disrupted ciliogenesis in Xenopus epidermal MCCs. Subcellular analysis revealed a striking impairment of basal body docking and spacing, which is likely to account for the observed phenotypes. These results are substantiated by showing a genetic interaction between elmo1 and ezrin b. Finally, we provide biochemical evidence that the ELMO-DOCK1-Rac1 complex influences Ezrin phosphorylation and thereby probably serves as an important molecular switch. Collectively, we demonstrate that the ELMO-Ezrin complex orchestrates ciliary basal body migration, docking and positioning in vivo. PMID:25516973

  18. Recovery of post stroke proximal arm function, driven by complex neuroplastic bilateral brain activation patterns and predicted by baseline motor dysfunction severity

    Directory of Open Access Journals (Sweden)

    Svetlana ePundik

    2015-07-01

    Full Text Available Objectives: Neuroplastic changes that drive recovery of shoulder/elbow function after stoke have been poorly understood. The purpose of this study was to determine the relationship between neuroplastic brain changes related to shoulder/elbow movement control in response to treatment and recovery of arm motor function in chronic stroke survivors. Methods: Twenty-three chronic stroke survivors were treated with 12 weeks of arm rehabilitation. Outcome measures included functional Magnetic Resonance Imaging (fMRI for the shoulder/elbow components of reach and a skilled motor function test (Arm Motor Abilities Test (AMAT, collected before and after treatment.Results: We observed two patterns of neuroplastic changes that were associated with gains in motor function: decreased or increased task-related brain activation. Those with significantly better motor function at baseline exhibited a decrease in brain activation in response to treatment, evident in the ipsilesional primary motor and contralesional supplementary motor regions; in contrast, those with greater baseline motor impairment, exhibited increased brain activation in response to treatment. There was an linear relationship between greater functional gain (AMAT and increased activation in bilateral primary motor, contralesional primary and secondary sensory regions, and contralesional lateral premotor area, after adjusting for baseline AMAT, age, and time since stroke. Conclusions: Recovery of functional reach involves recruitment of several contralesional and bilateral primary motor regions. In response to intensive therapy, the direction of functional brain change (i.e. increase or decrease in task-related brain recruitment for shoulder/elbow reach components depends on baseline level of motor function and may represent either different phases or different strategies of neuroplasticity that drive functional recovery.

  19. Kennedy Space Center (KSC) Launch Complex 39 (LC-39) Gaseous Hydrogen (GH2) Vent Arm Behavior Prediction Model Review Technical Assessment Report

    Science.gov (United States)

    Wilson, Timmy R.; Beech, Geoffrey; Johnston, Ian

    2009-01-01

    The NESC Assessment Team reviewed a computer simulation of the LC-39 External Tank (ET) GH2 Vent Umbilical system developed by United Space Alliance (USA) for the Space Shuttle Program (SSP) and designated KSC Analytical Tool ID 451 (KSC AT-451). The team verified that the vent arm kinematics were correctly modeled, but noted that there were relevant system sensitivities. Also, the structural stiffness used in the math model varied somewhat from the analytic calculations. Results of the NESC assessment were communicated to the model developers.

  20. DOTASA, an Asymmetrical Derivative of DOTA Substituted at one Acetate pendant Arm: 1H NMR and Potentiometric Studies of the Ligand and its Lanthanide(III) Complexes

    OpenAIRE

    André, João P.; Brücher, Ernö; Kiraly, Robert; Carvalho, Rui A.; Mäcke, Helmut; Geraldes, Carlos F. G. C.

    2005-01-01

    The ligand H5dotasa (=(alphaRS)-alpha-(carboxymethyl)-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) is a H4dota-like macrocyclic ligand with a carboxymethyl CH2COOH substituent moiety at the C(alpha) atom of one of the four acetate pendant arms of H4dota (=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid), present as a racemic mixture of (alphaR) and (alphaS) enantiomers. The protonation constants of the ligand were determined by potentiometry, giving values close to H4dot...

  1. Differential regulation of synaptic vesicle tethering and docking by UNC-18 and TOM-1

    Directory of Open Access Journals (Sweden)

    Elena O Gracheva

    2010-10-01

    Full Text Available The assembly of SNARE complexes between syntaxin, SNAP-25 and synaptobrevin is required to prime synaptic vesicles for fusion. Since Munc18 and tomosyn compete for syntaxin interactions, the interplay between these proteins is predicted to be important in regulating synaptic transmission. We explored this possibility, by examining genetic interactions between C. elegans unc-18(Munc18, unc-64(syntaxin and tom-1(tomosyn. We have previously demonstrated that unc-18 mutants have reduced synaptic transmission, whereas tom-1 mutants exhibit enhanced release. Here we show that the unc-18 mutant release defect is associated with loss of two morphologically distinct vesicle pools; those tethered within 25nm of the plasma membrane and those docked with the plasma membrane. In contrast, priming defective unc-13 mutants accumulate tethered vesicles, while docked vesicles are greatly reduced, indicating tethering is UNC-18-dependent and occurs in the absence of priming. C. elegans unc-64 mutants phenocopy unc-18 mutants, losing both tethered and docked vesicles, whereas overexpression of open syntaxin preferentially increases vesicle docking, suggesting UNC-18/closed syntaxin interactions are responsible for vesicle tethering. Given the competition between vertebrate tomosyn and Munc18, for syntaxin binding, we hypothesized that C. elegans TOM-1 may inhibit both UNC-18-dependent vesicle targeting steps. Consistent with this hypothesis, tom-1 mutants exhibit enhanced UNC-18 plasma membrane localization and a concomitant increase in both tethered and docked synaptic vesicles. Furthermore, in tom-1;unc-18 double mutants the docked, primed vesicle pool is preferentially rescued relative to unc-18 single mutants. Together these data provide evidence for the differential regulation of two vesicle targeting steps by UNC-18 and TOM-1 through competitive interactions with syntaxin

  2. Resident CAPS on dense-core vesicles docks and primes vesicles for fusion.

    Science.gov (United States)

    Kabachinski, Greg; Kielar-Grevstad, D Michelle; Zhang, Xingmin; James, Declan J; Martin, Thomas F J

    2016-02-15

    The Ca(2+)-dependent exocytosis of dense-core vesicles in neuroendocrine cells requires a priming step during which SNARE protein complexes assemble. CAPS (aka CADPS) is one of several factors required for vesicle priming; however, the localization and dynamics of CAPS at sites of exocytosis in live neuroendocrine cells has not been determined. We imaged CAPS before, during, and after single-vesicle fusion events in PC12 cells by TIRF micro-scopy. In addition to being a resident on cytoplasmic dense-core vesicles, CAPS was present in clusters of approximately nine molecules near the plasma membrane that corresponded to docked/tethered vesicles. CAPS accompanied vesicles to the plasma membrane and was present at all vesicle exocytic events. The knockdown of CAPS by shRNA eliminated the VAMP-2-dependent docking and evoked exocytosis of fusion-competent vesicles. A CAPS(ΔC135) protein that does not localize to vesicles failed to rescue vesicle docking and evoked exocytosis in CAPS-depleted cells, showing that CAPS residence on vesicles is essential. Our results indicate that dense-core vesicles carry CAPS to sites of exocytosis, where CAPS promotes vesicle docking and fusion competence, probably by initiating SNARE complex assembly. PMID:26700319

  3. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand

    Science.gov (United States)

    DeLuca, Samuel; Khar, Karen; Meiler, Jens

    2015-01-01

    RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand) making it unfeasible for use in virtual High Throughput Screening (vHTS). To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial ‘low-resolution’ docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10–15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the ‘high-resolution’ full atom refinement step. PMID:26207742

  4. Laser space rendezvous and docking tradeoff

    Science.gov (United States)

    Adelman, S.; Levinson, S.; Raber, P.; Weindling, F.

    1974-01-01

    A spaceborne laser radar (LADAR) was configured to meet the requirements for rendezvous and docking with a cooperative object in synchronous orbit. The LADAR, configurated using existing pulsed CO2 laser technology and a 1980 system technology baseline, is well suited for the envisioned space tug missions. The performance of a family of candidate LADARS was analyzed. Tradeoff studies as a function of size, weight, and power consumption were carried out for maximum ranges of 50, 100, 200, and 300 nautical miles. The investigation supports the original contention that a rendezvous and docking LADAR can be constructed to offer a cost effective and reliable solution to the envisioned space missions. In fact, the CO2 ladar system offers distinct advantages over other candidate systems.

  5. MSFC Three Point Docking Mechanism design review

    Science.gov (United States)

    Schaefer, Otto; Ambrosio, Anthony

    1992-12-01

    In the next few decades, we will be launching expensive satellites and space platforms that will require recovery for economic reasons, because of initial malfunction, servicing, repairs, or out of a concern for post lifetime debris removal. The planned availability of a Three Point Docking Mechanism (TPDM) is a positive step towards an operational satellite retrieval infrastructure. This study effort supports NASA/MSFC engineering work in developing an automated docking capability. The work was performed by the Grumman Space & Electronics Group as a concept evaluation/test for the Tumbling Satellite Retrieval Kit. Simulation of a TPDM capture was performed in Grumman's Large Amplitude Space Simulator (LASS) using mockups of both parts (the mechanism and payload). Similar TPDM simulation activities and more extensive hardware testing was performed at NASA/MSFC in the Flight Robotics Laboratory and Space Station/Space Operations Mechanism Test Bed (6-DOF Facility).

  6. Concepts to Automate Fluid Transfer Capability of Low Impact Docking System (LIDS)

    Science.gov (United States)

    Miernik, Janie H.; Lukens, Scott; Robertson, Jeff

    2005-01-01

    The capability to transfer mass between spacecraft is necessary for many mission scenarios. Docking and berthing operations have enabled fluid, electrical, crew and equipment transfers to some degree on all manned space operations since the Gemini program. The Apollo program performed some sophisticated docking maneuvers to land men on the moon and return them safely to Earth. These programs primarily transferred crew, equipment, and pressurized atmosphere between docked spacecraft. The International Space Station (ISS) U.S. modules are connected by Common Berthing Mechanism (CBM) portals. They provide many feed-through ports for electrical, and fluid transfer between modules, as well as a large diameter crew and equipment tunnel. Fluid and electrical jumpers are manually installed after the CBM sealing surfaces have been securely mated to maintain the pressurized cabin environment. CBM berthing and subsequent fluid transfer capability requires a lengthy manual process involving an active interface that mates with a passive half. The Androgynous Peripheral Attach System (MAS) a Russian technology that docked the Russian Zarya module to Unity, or Node 1, is a more complex system that also is capable of fuel transfer, enabling refueling of the Russian re-boost engines on ISS. For several years, a Low Impact Docking System (LIDS) has been under development at Johnson Space Center (JSC). This docking technology has a requirement to be androgynous in order to allow the fabrication of a single configuration that can dock with all other LIDS units. It is desired to make electrical and fluid coupling mating an automated process to enable routine docking and undocking operations to support future exploration missions. It is envisioned that modular design and vehicle assembly will require an efficient LIDS for fuel, electrical, crew, and equipment transfer. Marshall Space Flight Center (MSFC) has joined the LIDS development effort and plans to employ fluid transfer concepts

  7. MOLECULAR DOCKING, SINTESIS dan UJI AKTIVITAS SITOTOKSIK

    Directory of Open Access Journals (Sweden)

    Dian Agung Pangaribowo

    2014-06-01

    Full Text Available ABSTRAK: Senyawa 1-benzoil-1,3-dimetilurea telah dirancang, disintesis, diidentifikasi struktur, dan diuji aktivitas sitotoksik secara in vitro. Simulasi docking dilakukan dengan memposisikan senyawa ke dalam sisi aktif reseptor Checkpoint kinase 1 (Chk1 untuk menentukan model pengikatan ligan reseptor. Sintesis 1-benzoil-1,3-dimetilurea dilakukan lewat reaksi asilasi antara 1,3-dimetilurea dan benzoil klorida. Kemurnian produk hasil sintesis ditentukan dengan metode Kromatografi Lapis Tipis (KLT. Identifikasi struktur dilakukan dengan spektrofotometer UV, FT-IR dan spektrometer NMR. Hasil uji antiproliferatif menunjukkan bahwa senyawa 1-benzoil-1,3-dimetilurea memiliki aktivitas sitotoksik terhadap sel HeLa yang lebih baik dibandingkan dengan kontrol positif. Senyawa 1-benzoil-1,3-dimetilurea dengan aktivitas sitotoksik dapat menjadi agen antikanker yang potensial. Kata kunci: 1-benzoil-1,3-dimetilurea, molecular docking, aktivitas sitotoksik ABSTRACT: A novel 1-benzoyl-1,3-dimethylurea has been designed, synthesized, structurally determined, and the in vitro cytotoxic activity was evaluated. Docking simulation was performed to position this compound into the Checkpoint kinase 1 (Chk1 active site to determine the probable binding model. Synthesis of 1-benzoyl-1,3-dimethylurea was completed by acylation reaction between 1,3-dimethylurea and benzoyl chloride. The purity of synthesized product was determined by Thin Layer Chromatography. Structure identification was performed by UV spectrophotometer, FT-IR and NMR spectrometer. Antiproliferative assay result demonstrated that this compound possessed good cytotoxic activity against HeLa cells, which is comparable to the positive control. This compound with potent cytotoxic activity might be a potential anticancer agent. Keywords: 1-benzoyl-1,3-dimethylurea, molecular docking, cytotoxic activity

  8. Protein-Protein Interaction Analysis by Docking

    OpenAIRE

    Stephan Ederer; Florian Fink; Wolfram Gronwald

    2009-01-01

    Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general applicability of our approach.

  9. Effects of tail docking and docking length on neuroanatomical changes in healed tail tips of pigs

    DEFF Research Database (Denmark)

    Herskin, M S; Thodberg, K; Jensen, Henrik Elvang

    2015-01-01

    In pig production, piglets are tail docked at birth in order to prevent tail biting later in life. In order to examine the effects of tail docking and docking length on the formation of neuromas, we used 65 pigs and the following four treatments: intact tails (n=18); leaving 75% (n=17); leaving 50......% (n=19); or leaving 25% (n=11) of the tail length on the pigs. The piglets were docked between day 2 and 4 after birth using a gas-heated apparatus, and were kept under conventional conditions until slaughter at 22 weeks of age, where tails were removed and examined macroscopically and histologically....... The tail lengths and diameters differed at slaughter (lengths: 30.6±0.6; 24.9±0.4; 19.8±0.6; 8.7±0.6 cm; P<0.001; tail diameter: 0.5±0.03; 0.8±0.02; 1.0±0.03; 1.4±0.04 cm; P<0.001, respectively). Docking resulted in a higher proportion of tails with neuromas (64 v. 0%; P<0.001), number of neuromas per...

  10. Effects of tail docking and docking length on neuroanatomical changes in healed tail tips of pigs.

    Science.gov (United States)

    Herskin, M S; Thodberg, K; Jensen, H E

    2015-04-01

    In pig production, piglets are tail docked at birth in order to prevent tail biting later in life. In order to examine the effects of tail docking and docking length on the formation of neuromas, we used 65 pigs and the following four treatments: intact tails (n=18); leaving 75% (n=17); leaving 50% (n=19); or leaving 25% (n=11) of the tail length on the pigs. The piglets were docked between day 2 and 4 after birth using a gas-heated apparatus, and were kept under conventional conditions until slaughter at 22 weeks of age, where tails were removed and examined macroscopically and histologically. The tail lengths and diameters differed at slaughter (lengths: 30.6±0.6; 24.9±0.4; 19.8±0.6; 8.7±0.6 cm; Ptail diameter: 0.5±0.03; 0.8±0.02; 1.0±0.03; 1.4±0.04 cm; Ptails with neuromas (64 v. 0%; Ptail (1.0±0.2 v. 0; Ptail docking piglets using hot-iron cautery causes formation of neuromas in the outermost part of the tail tip. The presence of neuromas might lead to altered nociceptive thresholds, which need to be confirmed in future studies. PMID:25482535

  11. Most Correlated Arms Identification

    OpenAIRE

    Liu, Che-Yu; Bubeck, Sébastien

    2014-01-01

    We study the problem of finding the most mutually correlated arms among many arms. We show that adaptive arms sampling strategies can have significant advantages over the non-adaptive uniform sampling strategy. Our proposed algorithms rely on a novel correlation estimator. The use of this accurate estimator allows us to get improved results for a wide range of problem instances.

  12. HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches.

    Science.gov (United States)

    Huang, Sheng-You; Li, Min; Wang, Jianxin; Pan, Yi

    2016-06-27

    Structure-based molecular docking and ligand-based similarity search are two commonly used computational methods in computer-aided drug design. Structure-based docking tries to utilize the structural information on a drug target like protein, and ligand-based screening takes advantage of the information on known ligands for a target. Given their different advantages, it would be desirable to use both protein- and ligand-based approaches in drug discovery when information for both the protein and known ligands is available. Here, we have presented a general hybrid docking protocol, referred to as HybridDock, to utilize both the protein structures and known ligands by combining the molecular docking program MDock and the ligand-based similarity search method SHAFTS, and evaluated our hybrid docking protocol on the CSAR 2013 and 2014 exercises. The results showed that overall our hybrid docking protocol significantly improved the performance in both binding affinity and binding mode predictions, compared to the sole MDock program. The efficacy of the hybrid docking protocol was further confirmed using the combination of DOCK and SHAFTS, suggesting an alternative docking approach for modern drug design/discovery. PMID:26317502

  13. Conceptual design of the hot cell facility universal docking station at ITER

    International Nuclear Information System (INIS)

    Between main shutdowns of the ITER machine, in-vessel components and Iter Remote Maintenance System (IRMS) are transferred between the Tokamak complex and the Hot Cell Facility using different types of sealed casks. Transfer Casks have different physical interfaces with the Vacuum Vessel, which need to be the same at the docking stations of the HCF. It means that in-vessel components and IRMS are cleaned in the same cells, which is in fact not convenient. Furthermore, logistic studies showed that the use rate of the cells is very inhomogeneous. In order to have dedicated cell for decontamination of Remote Handling tools, in order to increase the operability efficiency and to removes the hot cell docking operation from the critical path, the concept of a universal docking station has been investigated. Based on an existing design, the work was focused on a review of requirements, the re-design and the integration within the HCF layout. The universal docking station has been proposed and is now integrated in HCF design.

  14. Conceptual design of the hot cell facility universal docking station at ITER

    Energy Technology Data Exchange (ETDEWEB)

    Dammann, A., E-mail: alexis.dammann@iter.org [ITER Organization, CS 90 046, 13067 St Paul Lez Durance Cedex (France); Benchikhoune, M.; Friconneau, J.P.; Ivanov, V. [ITER Organization, CS 90 046, 13067 St Paul Lez Durance Cedex (France); Lemee, A. [SOGETI High Tech, 180 Rue Rene Descartes, 13851 Aix en Provence (France); Martins, J.P. [ITER Organization, CS 90 046, 13067 St Paul Lez Durance Cedex (France); Tamassy, G. [SOGETI High Tech, 180 Rue Rene Descartes, 13851 Aix en Provence (France)

    2011-10-15

    Between main shutdowns of the ITER machine, in-vessel components and Iter Remote Maintenance System (IRMS) are transferred between the Tokamak complex and the Hot Cell Facility using different types of sealed casks. Transfer Casks have different physical interfaces with the Vacuum Vessel, which need to be the same at the docking stations of the HCF. It means that in-vessel components and IRMS are cleaned in the same cells, which is in fact not convenient. Furthermore, logistic studies showed that the use rate of the cells is very inhomogeneous. In order to have dedicated cell for decontamination of Remote Handling tools, in order to increase the operability efficiency and to removes the hot cell docking operation from the critical path, the concept of a universal docking station has been investigated. Based on an existing design, the work was focused on a review of requirements, the re-design and the integration within the HCF layout. The universal docking station has been proposed and is now integrated in HCF design.

  15. The DOCK protein sponge binds to ELMO and functions in Drosophila embryonic CNS development.

    Directory of Open Access Journals (Sweden)

    Bridget Biersmith

    Full Text Available Cell morphogenesis, which requires rearrangement of the actin cytoskeleton, is essential to coordinate the development of tissues such as the musculature and nervous system during normal embryonic development. One class of signaling proteins that regulate actin cytoskeletal rearrangement is the evolutionarily conserved CDM (C. elegansCed-5, human DOCK180, DrosophilaMyoblast city, or Mbc family of proteins, which function as unconventional guanine nucleotide exchange factors for the small GTPase Rac. This CDM-Rac protein complex is sufficient for Rac activation, but is enhanced upon the association of CDM proteins with the ELMO/Ced-12 family of proteins. We identified and characterized the role of Drosophila Sponge (Spg, the vertebrate DOCK3/DOCK4 counterpart as an ELMO-interacting protein. Our analysis shows Spg mRNA and protein is expressed in the visceral musculature and developing nervous system, suggesting a role for Spg in later embryogenesis. As maternal null mutants of spg die early in development, we utilized genetic interaction analysis to uncover the role of Spg in central nervous system (CNS development. Consistent with its role in ELMO-dependent pathways, we found genetic interactions with spg and elmo mutants exhibited aberrant axonal defects. In addition, our data suggests Ncad may be responsible for recruiting Spg to the membrane, possibly in CNS development. Our findings not only characterize the role of a new DOCK family member, but help to further understand the role of signaling downstream of N-cadherin in neuronal development.

  16. A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.

    Science.gov (United States)

    Gong, Xin Qi; Chang, Shan; Zhang, Qing Hua; Li, Chun Hua; Shen, Long Zhu; Ma, Xiao Hui; Wang, Ming Hui; Liu, Bin; He, Hong Qiu; Chen, Wei Zu; Wang, Cun Xin

    2007-12-01

    Protein-protein docking is usually exploited with a two-step strategy, i.e., conformational sampling and decoy scoring. In this work, a new filter enhanced sampling scheme was proposed and added into the RosettaDock algorithm to improve the conformational sampling efficiency. The filter term is based on the statistical result that backbone hydrogen bonds in the native protein structures are wrapped by more than nine hydrophobic groups to shield them from attacks of water molecules (Fernandez and Scheraga, Proc Natl Acad Sci USA 2003;100:113-118). A combinatorial scoring function, ComScore, specially designed for the other-type protein-protein complexes was also adopted to select the near native docked modes. ComScore was composed of the atomic contact energy, van der Waals, and electrostatic interaction energies, and the weight of each item was fit through the multiple linear regression approach. To analyze our docking results, the filter enhanced sampling scheme was applied to targets T12, T20, and T21 after the CAPRI blind test, and improvements were obtained. The ligand least root mean square deviations (L_rmsds) were reduced and the hit numbers were increased. ComScore was used in the scoring test for CAPRI rounds 9-12 with good success in rounds 9 and 11. PMID:17803223

  17. Docking Screens for Novel Ligands Conferring New Biology.

    Science.gov (United States)

    Irwin, John J; Shoichet, Brian K

    2016-05-12

    It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years. PMID:26913380

  18. The arms race control

    International Nuclear Information System (INIS)

    Written in 1961, this paper presents the content of a book entitled 'The arms race control' where the author outlined the difference between disarmament and arms control, described the economic and moral role of arms race, the importance of force balance for international security. He wandered whether arms control could ensure this balance and whether nuclear balance meant force balance. Force balance then appears to be a precarious and unsteady component of international security. He commented the challenges of disarmament, recalled some arguments for a nuclear disarmament. Then he discussed what would be an arms control with or without disarmament (either nuclear or conventional)

  19. Late First-Row Transition-Metal Complexes Containing a 2-Pyridylmethyl Pendant-Armed 15-Membered Macrocyclic Ligand. Field-Induced Slow Magnetic Relaxation in a Seven-Coordinate Cobalt(II) Compound.

    Science.gov (United States)

    Antal, Peter; Drahoš, Bohuslav; Herchel, Radovan; Trávníček, Zdeněk

    2016-06-20

    The 2-pyridylmethyl N-pendant-armed heptadentate macrocyclic ligand {3,12-bis(2-methylpyridine)-3,12,18-triaza-6,9-dioxabicyclo[12.3.1]octadeca-1,14,16-triene = L} and [M(L)](ClO4)2 complexes, where M = Mn(II) (1), Fe(II) (2), Co(II) (3), Ni(II) (4), and Cu(II) (5), were prepared and thoroughly characterized, including elucidation of X-ray structures of all the compounds studied. The complexes 1-5 crystallize in non-centrosymmetric Sohncke space groups as racemic compounds. The coordination numbers of 7, 6 + 1, and 5 were found in complexes 1-3, 4, and 5, respectively, with a distorted pentagonal bipyramidal (1-4) or square pyramidal (5) geometry. On the basis of the magnetic susceptibility experiments, a large axial zero-field splitting (ZFS) was found for 2, 3, and 4 (D(Fe) = -7.4(2) cm(-1), D(Co) = 34(1) cm(-1), and D(Ni) = -12.8(1) cm(-1), respectively) together with a rhombic ZFS (E/D = 0.136(3)) for 4. Despite the easy plane anisotropy (D > 0, E/D = 0) in 3, the slow relaxation of the magnetization below 8 K was observed and analyzed either with Orbach relaxation mechanism (the relaxation time τ0 = 9.90 × 10(-10) s and spin reversal barrier Ueff = 24.3 K (16.9 cm(-1))) or with Raman relaxation mechanism (C = 2.12 × 10(-5) and n = 2.84). Therefore, compound 3 enlarges the small family of field-induced single-molecule magnets with pentagonal-bipyramidal chromophore. The cyclic voltammetry in acetonitrile revealed reversible redox processes in 1-3 and 5, except for the Ni(II) complex 4, where a quasi-reversible process was dominantly observed. Presence of the two 2-pyridylmethyl pendant arms in L with a stronger σ-donor/π-acceptor ability had a great impact on the properties of all the complexes (1-5), concretely: (i) strong pyridine-metal bonds provided slight axial compression of the coordination sphere, (ii) substantial changes in magnetic anisotropy, and (iii) stabilization of lower oxidation states. PMID:27245288

  20. Dock protein family in brain development and neurological disease

    OpenAIRE

    Shi, Lei

    2013-01-01

    The family of dedicator of cytokinesis (Dock), a protein family that belongs to the atypical Rho guanine nucleotide exchange factors (GEFs) for Rac and/or Cdc42 GTPases, plays pivotal roles in various processes of brain development. To date, 11 members of Docks have been identified in the mammalian system. Emerging evidence has suggested that members of the Dock family are associated with several neurodegenerative and neuropsychiatric diseases, including Alzheimer disease and autism spectrum ...

  1. Cembrene Diterpenoids: Conformational Studies and Molecular Docking to Tubulin

    Directory of Open Access Journals (Sweden)

    Heather E. Villanueva

    2010-04-01

    Full Text Available A conformational analysis of the cembrene diterpenoids cembrene, cembrene A, (3Z-cembrene A, isocembrene, casbene, and incensole, has been carried out using density functional theory at the B3LYP/6-31G* level of theory. A molecular docking analysis of these cembrenoids with tubulin has also been performed in order to assess the potential of tubulin binding of these cytotoxic agents. The macrocyclic cembrenoids are conformationally mobile and numerous low-energy conformations were found. Molecular docking reveals that the cembrenoids dock into the colchicine binding site of tubulin with comparable docking energies to colchicine.

  2. A Review: Mathematical Modles for Cross Docking Planning

    Directory of Open Access Journals (Sweden)

    Dwi Agustina

    2010-09-01

    Full Text Available This paper provides a comprehensive literature review of mathematical models in cross docking planning. From the reviews, the models are classified in three different levels regarding its decisions level which are operational, tactical, and strategic level. The researches in operational level are mainly related to develop model in scheduling, dock door assignment, transhipment problem, vehicle routing, and product allocation. For tactical and strategic level, the researches are mainly proposing model to design the layout and the network of cross docking respectively. The contribution of this paper is to realize the gaps of knowledge in strategic, tactical and operational levels and point out the future research directions in cross docking.

  3. Complexity

    CERN Document Server

    Gershenson, Carlos

    2011-01-01

    The term complexity derives etymologically from the Latin plexus, which means interwoven. Intuitively, this implies that something complex is composed by elements that are difficult to separate. This difficulty arises from the relevant interactions that take place between components. This lack of separability is at odds with the classical scientific method - which has been used since the times of Galileo, Newton, Descartes, and Laplace - and has also influenced philosophy and engineering. In recent decades, the scientific study of complexity and complex systems has proposed a paradigm shift in science and philosophy, proposing novel methods that take into account relevant interactions.

  4. Synthesis, Characterization, and Biological Activities of Pendant Arm-Pyridyltetrazole Copper(II) Complexes: DNA Binding/Cleavage Activity and Cytotoxic Studies.

    Science.gov (United States)

    Mustafa, Shaik; Rao, Bommuluri Umamaheswara; Surendrababu, Manubolu Surya; Raju, Kalidindi Krishnam; Rao, Gollapalli Nageswara

    2015-10-01

    2-(1H-Tetrazol-5-yl)pyridine (L) has been reacted separately with Me2NCH2CH2Cl⋅HCl and ClCH2CH2OH to yield two regioisomers in each case, N,N-dimethyl-2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanamine (L1)/N,N-dimethyl-2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanamine (L2) and 2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanol (L3)/2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanol (L4), respectively. These ligands, L1-L4, have been coordinated with CuCl2 ⋅H2O in 1 : 1 composition to furnish the corresponding complexes 1-4. EPR Spectra of Cu complexes 1 and 3 were characteristic of square planar geometry, with nuclear hyperfine spin 3/2. Single X-ray crystallographic studies of 3 revealed that the Cu center has a square planar structure. DNA binding studies were carried out by UV/VIS absorption; viscosity and thermal denaturation studies revealed that each of these complexes are avid binders of calf thymus DNA. Investigation of nucleolytic cleavage activities of the complexes was carried out on double-stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment under various conditions, where cleavage of DNA takes place by oxidative free-radical mechanism (OH(⋅)). In vitro anticancer activities of the complexes against MCF-7 (human breast adenocarcinoma) cells revealed that the complexes inhibit the growth of cancer cells. The IC50 values of the complexes showed that Cu complexes exhibit comparable cytotoxic activities compared to the standard drug cisplatin. PMID:26460557

  5. DockAnalyse: an application for the analysis of protein-protein interactions

    OpenAIRE

    Cedano Juan; Querol Enrique; Bonàs Sílvia; Gómez Antonio; Delicado Pedro; Amela Isaac

    2010-01-01

    Abstract Background Is it possible to identify what the best solution of a docking program is? The usual answer to this question is the highest score solution, but interactions between proteins are dynamic processes, and many times the interaction regions are wide enough to permit protein-protein interactions with different orientations and/or interaction energies. In some cases, as in a multimeric protein complex, several interaction regions are possible among the monomers. These dynamic pro...

  6. Robust Design of Docking Hoop for Recovery of Autonomous Underwater Vehicle with Experimental Results

    OpenAIRE

    Wei Peng Lin; Cheng Siong Chin; Leonard Chin Wai Looi; Jun Jie Lim; Elvin Min Ee Teh

    2015-01-01

    Control systems prototyping is usually constrained by model complexity, embedded system configurations, and interface testing. The proposed control system prototyping of a remotely-operated vehicle (ROV) with a docking hoop (DH) to recover an autonomous underwater vehicle (AUV) named AUVDH using a combination of software tools allows the prototyping process to be unified. This process provides systematic design from mechanical, hydrodynamics, dynamics modelling, control system design, and sim...

  7. A coarse-grained force field for Protein–RNA docking

    OpenAIRE

    Setny, Piotr; Zacharias, Martin

    2011-01-01

    The awareness of important biological role played by functional, non coding (nc) RNA has grown tremendously in recent years. To perform their tasks, ncRNA molecules typically unite with protein partners, forming ribonucleoprotein complexes. Structural insight into their architectures can be greatly supplemented by computational docking techniques, as they provide means for the integration and refinement of experimental data that is often limited to fragments of larger assemblies or represents...

  8. A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

    OpenAIRE

    Bourquard, Thomas; Bernauer, Julie; Azé, Jérôme; Poupon, Anne

    2011-01-01

    A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in...

  9. Design und Betrieb von Cross Docks

    OpenAIRE

    Sinja-Katharina Tiedemann; Nils Boysen

    2009-01-01

    Die hohen Anforderungen an heutige Wertschöpfungsnetzwerke in Bezug auf Flexibilität und Lieferbereitschaft stellen die Distribution vor die Aufgabe, Güter immer häufiger und in immer kleineren Mengen ausliefern zu müssen. Ein Ansatz, diesen Forderungen auf möglichst wirtschaftliche Art und Weise gerecht zu werden, besteht darin, bestehende Distributionsnetze um sogenannte Cross Docks zu erweitern. In solchen lagerlosen Umschlagzentren können dann kleine Warensendungen mit ähnlicher Destinati...

  10. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

    Directory of Open Access Journals (Sweden)

    Vakser Ilya A

    2011-07-01

    Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

  11. S4MPLE--sampler for multiple protein-ligand entities: simultaneous docking of several entities.

    Science.gov (United States)

    Hoffer, Laurent; Horvath, Dragos

    2013-01-28

    S4MPLE is a conformational sampling tool, based on a hybrid genetic algorithm, simulating one (conformer enumeration) or more molecules (docking). Energy calculations are based on the AMBER force field [Cornell et al. J. Am. Chem. Soc. 1995, 117, 5179.] for biological macromolecules and its generalized version GAFF [Wang et al. J. Comput. Chem. 2004 , 25, 1157.] for ligands. This paper describes more advanced, specific applications of S4MPLE to problems more complex than classical redocking of drug-like compounds [Hoffer et al. J. Mol. Graphics Modell. 2012, submitted for publication.]. Here, simultaneous docking of multiple entities is addressed in two different important contexts. First, simultaneous docking of two fragment-like ligands was attempted, as such ternary complexes are the basis of fragment-based drug design by linkage of the independent binders. As a preliminary, the capacity of S4MPLE to dock fragment-like compounds has been assessed, since this class of small probes used in fragment-based drug design covers a different chemical space than drug-like molecules. Herein reported success rates from fragments redocking are as good as classical benchmarking results on drug-like compounds (Astex Diverse Set [Hartshorn et al. J. Med. Chem. 2007, 50, 726.]). Then, S4MPLE is successfully challenged to predict locations of fragments involved in ternary complexes by means of multientity docking. Second, the key problem of predicting water-mediated interaction is addressed by considering explicit water molecules as additional entities to be docked in the presence of the "main" ligand. Blind prediction of solvent molecule positions, reproducing relevant ligand-water-site mediated interactions, is achieved in 76% cases over saved poses. S4MPLE was also successful to predict crystallographic water displacement by a therefore tailored functional group in the optimized ligand. However, water localization is an extremely delicate issue in terms of weighing of

  12. Multilevel Parallelization of AutoDock 4.2

    Directory of Open Access Journals (Sweden)

    Norgan Andrew P

    2011-04-01

    Full Text Available Abstract Background Virtual (computational screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4. Results Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers. Conclusions Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI and node-level (OpenMP parallelization to best fit both workloads and computational resources.

  13. A Sliding Docking Interaction Is Essential for Sequential and Processive Phosphorylation of an SR Protein by SRPK1

    OpenAIRE

    Ngo, Jacky Chi Ki; Giang, Kayla; Chakrabarti, Sutapa; Ma, Chen-Ting; Huynh, Nhat; Hagopian, Jonathan C.; Dorrestein, Pieter C.; Fu, Xiang-Dong; Adams, Joseph A.; Ghosh, Gourisankar

    2008-01-01

    The 2.9 Å crystal structure of the core SRPK1:ASF/SF2 complex reveals that the N-terminal half of the basic RS domain of ASF/SF2, which is destined to be phosphorylated, is bound to an acidic docking groove of SRPK1 distal to the active site. Phosphorylation of ASF/SF2 at a single site in the C-terminal end of the RS domain generates a primed phosphoserine that binds to a basic site in the kinase. Biochemical experiments support a directional sliding of the RS peptide through the docking groo...

  14. An Overview of NASA's Asteroid Redirect Mission (ARM) Concept

    Science.gov (United States)

    Abell, P. A.; Mazanek, D. D.; Reeves, D. M.; Chodas, P. W.; Gates, M. M.; Johnson, L. N.; Ticker, R. L.

    2016-01-01

    The National Aeronautics and Space Administration (NASA) is developing the Asteroid Redirect Mission (ARM) as a capability demonstration for future human exploration, including use of high-power solar electric propulsion, which allows for the efficient movement of large masses through deep space. The ARM will also demonstrate the capability to conduct proximity operations with natural space objects and crewed operations beyond the security of quick Earth return. The Asteroid Redirect Robotic Mission (ARRM), currently in formulation, will visit a large near-Earth asteroid (NEA), collect a multi-ton boulder from its surface, conduct a demonstration of a slow push planetary defense technique, and redirect the multi-ton boulder into a stable orbit around the Moon. Once returned to cislunar space in the mid-2020s, astronauts aboard an Orion spacecraft will dock with the robotic vehicle to explore the boulder and return samples to Earth. The ARM is part of NASA's plan to advance technologies, capabilities, and spaceflight experience needed for a human mission to the Martian system in the 2030s. The ARM and subsequent availability of the asteroidal material in cis-lunar space, provide significant opportunities to advance our knowledge of small bodies in the synergistic areas of science, planetary defense, and in-situ resource utilization (ISRU). NASA established the Formulation Assessment and Support Team (FAST), comprised of scientists, engineers, and technologists, which supported ARRM mission requirements formulation, answered specific questions concerning potential target asteroid physical properties, and produced a publically available report. The ARM Investigation Team is being organized to support ARM implementation and execution. NASA is also open to collaboration with its international partners and welcomes further discussions. An overview of the ARM robotic and crewed segments, including mission requirements, NEA targets, and mission operations, and a discussion

  15. Targeting RING domains of Mdm2–MdmX E3 complex activates apoptotic arm of the p53 pathway in leukemia/lymphoma cells

    Science.gov (United States)

    Wu, W; Xu, C; Ling, X; Fan, C; Buckley, B P; Chernov, M V; Ellis, L; Li, F; Muñoz, I G; Wang, X

    2015-01-01

    Reactivation of tumor-suppressor p53 for targeted cancer therapy is an attractive strategy for cancers bearing wild-type (WT) p53. Targeting the Mdm2–p53 interface or MdmX ((MDM4), mouse double minute 4)–p53 interface or both has been a focus in the field. However, targeting the E3 ligase activity of Mdm2–MdmX really interesting new gene (RING)–RING interaction as a novel anticancer strategy has never been explored. In this report, we describe the identification and characterization of small molecule inhibitors targeting Mdm2–MdmX RING–RING interaction as a new class of E3 ligase inhibitors. With a fluorescence resonance energy transfer-based E3 activity assay in high-throughput screening of a chemical library, we identified inhibitors (designated as MMRis (Mdm2–MdmX RING domain inhibitors)) that specifically inhibit Mdm2–MdmX E3 ligase activity toward Mdm2 and p53 substrates. MMRi6 and its analog MMRi64 are capable of disrupting Mdm2–MdmX interactions in vitro and activating p53 in cells. In leukemia cells, MMRi64 potently induces downregulation of Mdm2 and MdmX. In contrast to Nutlin3a, MMRi64 only induces the expression of pro-apoptotic gene PUMA (p53 upregulated modulator of apoptosis) with minimal induction of growth-arresting gene p21. Consequently, MMRi64 selectively induces the apoptotic arm of the p53 pathway in leukemia/lymphoma cells. Owing to the distinct mechanisms of action of MMRi64 and Nutlin3a, their combination synergistically induces p53 and apoptosis. Taken together, this study reveals that Mdm2–MdmX has a critical role in apoptotic response of the p53 pathway and MMRi64 may serve as a new pharmacological tool for p53 studies and a platform for cancer drug development. PMID:26720344

  16. Modeling, Stability Analysis, and Testing of a Hybrid Docking Simulator

    OpenAIRE

    Zebenaya, M.; Boge, T.; Choukroun, D.

    2014-01-01

    A hybrid docking simulator is a hardware-in-the-loop (HIL) simulator that includes a hardware element within a numerical simulation loop. One of the goals of performing a HIL simulation at the European Proximity Operation Simulator (EPOS) is the verification and validation of the docking phase in an on-orbit servicing mission.....

  17. SpaceDock: A Performance Task Platform for Spaceflight Operations

    Science.gov (United States)

    Marshburn, Thomas H.; Strangman, Gary E.; Strauss, Monica S.; Sutton, Jeffrey P.

    2003-01-01

    Preliminary evidence during both short- and long-duration spaceflight indicates that perceptual-motor coordination changes occur and persist in-flight. However, there is presently no in-flight method for evaluating astronaut performance on mission-critical tasks such as docking. We present a portable platform we have developed for attempting and evaluating docking, and describe the results of a pilot study wherein flight novices learned the docking task. Methods: A dual-joystick, six degrees of freedom platform-called SpaceDock-was developed to enable portable, adaptable performance testing in a spaceflight operations setting. Upon this platform, a simplified docking task was created, involving a constant rate of approach towards a docking target and requiring the user to correct translation in two dimensions and attitude orientation along one dimension (either pitch or roll). Ten flight naive subjects performed the task over a 45 min period and all joystick inputs and timings were collected, from which we could successfully reconstruct travel paths, input profiles and relative target displacements. Results: Subjects exhibited significant improvements in docking over the course of the experiment. Learning to compensate for roll-alterations was robust, whereas compensation for pitch-alterations was not in evidence in this population and relatively short training period. Conclusion: The SpaceDock platform can provide a novel method for training and testing subjects, on a spaceflight-relevant task, and can be used to examine behavioral learning, strategy use, and has been adapted for use in brain imaging experiments.

  18. 18 CFR 1304.204 - Docks, piers, and boathouses.

    Science.gov (United States)

    2010-04-01

    ... structures due to extreme water level fluctuations. Roofs over docks or piers to provide shade are allowed on... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Docks, piers, and boathouses. 1304.204 Section 1304.204 Conservation of Power and Water Resources TENNESSEE VALLEY...

  19. A Sliding Docking Interaction Is Essential for Sequential and Processive Phosphorylation of an SR Protein by SRPK1

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Jacky Chi Ki; Giang, Kayla; Chakrabarti, Sutapa; Ma, Chen-Ting; Huynh, Nhat; Hagopian, Jonathan C.; Dorrestein, Pieter C.; Fu, Xiang-Dong; Adams, Joseph A.; Ghosh, Gourisankar (UCSD)

    2008-09-17

    The 2.9 {angstrom} crystal structure of the core SRPK1:ASF/SF2 complex reveals that the N-terminal half of the basic RS domain of ASF/SF2, which is destined to be phosphorylated, is bound to an acidic docking groove of SRPK1 distal to the active site. Phosphorylation of ASF/SF2 at a single site in the C-terminal end of the RS domain generates a primed phosphoserine that binds to a basic site in the kinase. Biochemical experiments support a directional sliding of the RS peptide through the docking groove to the active site during phosphorylation, which ends with the unfolding of a {beta} strand of the RRM domain and binding of the unfolded region to the docking groove. We further suggest that the priming of the first serine facilitates directional substrate translocation and efficient phosphorylation.

  20. Detecting Illegal Arms Trade

    OpenAIRE

    DellaVigna, Stefano; Ferrara, Eliana La

    2010-01-01

    Illegal arms are responsible for thousands of deaths in civil wars every year. Yet, their trade is very hard to detect. We propose a method to statistically detect illegal arms trade based on the investor knowledge embedded in financial markets. We focus on eight countries under UN arms embargo in the period 1990-2005, and analyze eighteen events during the embargo that suddenly increase or decrease conflict intensity. If the weapon-making companies are not trading or are trading legally, an ...

  1. Interaction of glutathione with bovine serum albumin: Spectroscopy and molecular docking.

    Science.gov (United States)

    Jahanban-Esfahlan, Ali; Panahi-Azar, Vahid

    2016-07-01

    This study aims to investigate the interaction between glutathione and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence spectroscopies under simulated physiological conditions (pH 7.4) and molecular docking methods. The results of fluorescence spectroscopy indicated that the fluorescence intensity of BSA was decreased considerably upon the addition of glutathione through a static quenching mechanism. The fluorescence quenching obtained was related to the formation of BSA-glutathione complex. The values of KSV, Ka and Kb for the glutathione and BSA interaction were in the order of 10(5). The thermodynamic parameters including enthalpy change (ΔH), entropy change (ΔS) and also Gibb's free energy (ΔG) were determined using Van't Hoff equation. These values showed that hydrogen bonding and van der Waals forces were the main interactions in the binding of glutathione to BSA and the stabilization of the complex. Also, the interaction of glutathione and BSA was spontaneous. The effects of glutathione on the BSA conformation were determined using UV-vis spectroscopy. Moreover, glutathione was docked in BSA using ArgusLab as a molecular docking program. It was recognized that glutathione binds within the sub-domain IIA pocket in domain II of BSA. PMID:26920314

  2. PERANCANGAN FLOATING DOCK UNTUK DAERAH PERAIRAN PELABUHAN KOTA TEGAL

    Directory of Open Access Journals (Sweden)

    Kiryanto Kiryanto

    2013-06-01

    Full Text Available Floating dock merupakan bangunan air sebagai tempat reparasi kapal yang dinilai cukup efisien dalam pembangunannya karena tidak membutuhkan dana yang terlalu mahal. Di sektor indusrti perkapalan kota tegal sudah memiliki galangan dan dock reparasi kapal yang cukup berkembang.  Ide perancangan floating dock ini dirancang sebagai alternatif baru pelayanan reparasi kapal. Perancangan floating dock ini juga memperhatikan dengan detail kapasitas kapal – kapal yang pernah melakukan repararasi di sekitar galangan di Kota Tegal agar ditemukan ukuran utama floating dock yang tepat. Dari Kapasitas kapal yang ada dan berdasarkan metode perbandingan ukuran beberapa floating dock, maka ditemukan ukuran utama yang tepat untuk menampung kebutuhan pelayanan reparasi kapal yaitu LOA = 136,37 m, Lpt = 114.80 m, Bmax = 36,40 m, Bmd: 30,80 m, Tmin = 0,86 m, Tmax = 1,58 m, Hpt = 2,10 m, HOA = 9,60 m. Berdasarkan perhitungan ditemukan juga Ton Lifting Capacity (TLC sebesar 3000 ton. Perancangan menggunakan software perkapalan yaitu dengan menggunakan AutoCad, Delftship, Maxsurf dan Hidromax. Dengan analisa stabilitas menggunakan software Hidromax diketahui bahwa floating dock ini mampu memiliki stabilitas yang baik dengan 4 kondisi yang semua memenuhi criteria  International Maritime Organisation (IMO. Perancangan floating dock ini juga menghitung analisa ekonomis dan investasi. Dari rekapitulasi dana investasi pembangunan floating dock yaitu sebesar Rp.136.622.888.000,00 dengan nilai kembali atau break even point selama 10 tahun dengan modal sendiri, 14 tahun dengan 50% modal sendiri dan 50 % pinjaman bank, dan break event point 18 tahun untuk dana pembangunan floating dock yang berasal dari 100 % pinjaman bank

  3. Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target?

    Science.gov (United States)

    Ramírez, David; Caballero, Julio

    2016-01-01

    Molecular docking is a computational chemistry method which has become essential for the rational drug design process. In this context, it has had great impact as a successful tool for the study of ligand-receptor interaction modes, and for the exploration of large chemical datasets through virtual screening experiments. Despite their unquestionable merits, docking methods are not reliable for predicting binding energies due to the simple scoring functions they use. However, comparisons between two or three complexes using the predicted binding energies as a criterion are commonly found in the literature. In the present work we tested how wise is it to trust the docking energies when two complexes between a target protein and enantiomer pairs are compared. For this purpose, a ligand library composed by 141 enantiomeric pairs was used, including compounds with biological activities reported against seven protein targets. Docking results using the software Glide (considering extra precision (XP), standard precision (SP), and high-throughput virtual screening (HTVS) modes) and AutoDock Vina were compared with the reported biological activities using a classification scheme. Our test failed for all modes and targets, demonstrating that an accurate prediction when binding energies of enantiomers are compared using docking may be due to chance. We also compared pairs of compounds with different molecular weights and found the same results. PMID:27104528

  4. Giant Polymersome Protocells Dock with Virus Particle Mimics via Multivalent Glycan-Lectin Interactions.

    Science.gov (United States)

    Kubilis, Artur; Abdulkarim, Ali; Eissa, Ahmed M; Cameron, Neil R

    2016-01-01

    Despite the low complexity of their components, several simple physical systems, including microspheres, coacervate droplets and phospholipid membrane structures (liposomes), have been suggested as protocell models. These, however, lack key cellular characteristics, such as the ability to replicate or to dock with extracellular species. Here, we report a simple method for the de novo creation of synthetic cell mimics in the form of giant polymeric vesicles (polymersomes), which are capable of behavior approaching that of living cells. These polymersomes form by self-assembly, under electroformation conditions, of amphiphilic, glycosylated block copolymers in aqueous solution. The glycosylated exterior of the resulting polymeric giant unilamellar vesicles (GUVs) allows their selective interaction with carbohydrate-binding receptor-functionalized particles, in a manner reminiscent of the cell-surface docking of virus particles. We believe that this is the first example of a simple protocell model displaying cell-like behavior through a native receptor-ligand interaction. PMID:27576579

  5. Probing the Interaction between Acotiamide Hydrochloride and Pepsin by Multispectral Methods, Electrochemical Measurements, and Docking Studies.

    Science.gov (United States)

    He, Jiawei; Ma, Xianglin; Wang, Qing; Huang, Yanmei; Li, Hui

    2016-07-01

    The interaction between acotiamide hydrochloride and pepsin was systematically characterized by fluorescence and electrochemical approaches. Fluorescence lifetime measurements showed that acotiamide hydrochloride quenched the intrinsic fluorescence of pepsin with a new complex formation via static mode, which was reconfirmed by cyclic voltammetry results. Both of the binding number and binding constants were calculated from differential pulse voltammetry analysis and fluorescence spectroscopy. The values obtained from the above two methods displayed a relatively high degree of consistency. Thermodynamic parameters suggested that acotiamide hydrochloride interacted with pepsin spontaneously by hydrogen bonding and van der Waals interactions. These results were consistent with the results obtained from molecular docking analysis. As revealed by synchronous fluorescence, three-dimensional fluorescence, Fourier transform infrared spectrometry, and circular dichroism spectra, acotiamide hydrochloride could affect the microenvironment and slightly change the secondary structure of pepsin. Furthermore, acotiamide hydrochloride can inhibit pepsin activity in vitro, as explained by the molecular docking. PMID:27018070

  6. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

    KAUST Repository

    Oliva, Romina

    2015-07-01

    In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

  7. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

    Directory of Open Access Journals (Sweden)

    Romina Oliva

    2015-07-01

    Full Text Available In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.

  8. THE POSITION OF RUSSIA IN THE WORLD ARMS MARKETS

    OpenAIRE

    Tuliakova I.R.

    2015-01-01

    The article is devoted to the role of Russia in the world arms market. Two world wars and arms race of the late twentieth century led to the formation of the defense- industrial complex. Russian military products are exported to many countries. Currently, Russia is the main supplier of arms to the world market. But there are serious limits to the expansion of military production

  9. Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search.

    Science.gov (United States)

    Hou, T; Wang, J; Chen, L; Xu, X

    1999-08-01

    A genetic algorithm (GA) combined with a tabu search (TA) has been applied as a minimization method to rake the appropriate associated sites for some biomolecular systems. In our docking procedure, surface complementarity and energetic complementarity of a ligand with its receptor have been considered separately in a two-stage docking method. The first stage was to find a set of potential associated sites mainly based on surface complementarity using a genetic algorithm combined with a tabu search. This step corresponds with the process of finding the potential binding sites where pharmacophores will bind. In the second stage, several hundreds of GA minimization steps were performed for each associated site derived from the first stage mainly based on the energetic complementarity. After calculations for both of the two stages, we can offer several solutions of associated sites for every complex. In this paper, seven biomolecular systems, including five bound complexes and two unbound complexes, were chosen from the Protein Data Bank (PDB) to test our method. The calculated results were very encouraging-the hybrid minimization algorithm successfully reaches the correct solutions near the best binded modes for these protein complexes. The docking results not only predict the bound complexes very well, but also get a relatively accurate complexed conformation for unbound systems. For the five bound complexes, the results show that surface complementarity is enough to find the precise binding modes, the top solution from the tabu list generally corresponds to the correct binding mode. For the two unbound complexes, due to the conformational changes upon binding, it seems more difficult to get their correct binding conformations. The predicted results show that the correct binding mode also corresponds to a relatively large surface complementarity score. In these two test cases, the correct solution can be found in the top several solutions from the tabu list. For

  10. DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations

    Science.gov (United States)

    Chakraborty, Sandeep

    2016-01-01

    The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a target protein, provided that there is at least one known holoenzyme with ligand bound - DOCLASP (Docking using CLASP). The contact points of the ligand in the holoenzyme defines a motif, which is used to query the target enzyme using CLASP. If there are significant matches, the holoenzyme and the target protein are superimposed based on congruent atoms. The same linear and rotational transformations are also applied to the ligand, thus creating a unified coordinate framework having the holoenzyme, the ligand and the target enzyme. In the current work, the dipeptidyl peptidase-IV inhibitor vildagliptin was docked to the PI-PLC structure complexed with myo-inositol using DOCLASP. Also, corroboration of the docking of phenylthiourea to the modelled structure of polyphenol oxidase (JrPPO1) from walnut is provided based on the subsequently solved structure of JrPPO1 (PDBid:5CE9). Analysis of the binding of the antitrypanosomial drug suramin to nine non-homologous proteins in the PDB database shows a diverse set of binding motifs, and multiple binding sites in the phospholipase A2-likeproteins from the Bothrops genus of pitvipers. The conformational changes in the suramin molecule on binding highlights the challenges in docking flexible ligands into an already ’plastic’ binding site. Thus, DOCLASP presents a method for ’soft docking’ ligands to proteins with low

  11. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility

    OpenAIRE

    Ravindranath, Pradeep Anand; Forli, Stefano; Goodsell, David S.; Olson, Arthur J.; Sanner, Michel F.

    2015-01-01

    Automated docking of drug-like molecules into receptors is an essential tool in structure-based drug design. While modeling receptor flexibility is important for correctly predicting ligand binding, it still remains challenging. This work focuses on an approach in which receptor flexibility is modeled by explicitly specifying a set of receptor side-chains a-priori. The challenges of this approach include the: 1) exponential growth of the search space, demanding more efficient search methods; ...

  12. ARM Mentor Selection Process

    Energy Technology Data Exchange (ETDEWEB)

    Sisterson, D. L. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-10-01

    The Atmospheric Radiation Measurement (ARM) Program was created in 1989 with funding from the U.S. Department of Energy (DOE) to develop several highly instrumented ground stations to study cloud formation processes and their influence on radiative transfer. In 2003, the ARM Program became a national scientific user facility, known as the ARM Climate Research Facility. This scientific infrastructure provides for fixed sites, mobile facilities, an aerial facility, and a data archive available for use by scientists worldwide through the ARM Climate Research Facility—a scientific user facility. The ARM Climate Research Facility currently operates more than 300 instrument systems that provide ground-based observations of the atmospheric column. To keep ARM at the forefront of climate observations, the ARM infrastructure depends heavily on instrument scientists and engineers, also known as lead mentors. Lead mentors must have an excellent understanding of in situ and remote-sensing instrumentation theory and operation and have comprehensive knowledge of critical scale-dependent atmospheric processes. They must also possess the technical and analytical skills to develop new data retrievals that provide innovative approaches for creating research-quality data sets. The ARM Climate Research Facility is seeking the best overall qualified candidate who can fulfill lead mentor requirements in a timely manner.

  13. Managing new arms races

    International Nuclear Information System (INIS)

    The management of new arms races in the region of Asia-Pacific includes considerations of weapons trade and transfer in the region, with an emphasis on nuclear weapons proliferation. It deals with the problem of controlling the arms trade and the efforts to control conventional weapons and underlines the possible role and influence of Conference on Cooperation and Security in Europe (CSCE)

  14. Dock treatment process : M/T King Darwin spill

    Energy Technology Data Exchange (ETDEWEB)

    Starkes, R. [Eastern Canada Response Corp. Ltd., Dartmouth, NS (Canada)

    2009-07-01

    This paper discussed the challenges that oil spill responder face when dealing with an incident on docks, piers and other marine structures. In September 2008, Bunker C fuel oil was spilled from the M/T King Darwin during the offloading operation when a pipe flange broke on the deck of the tanker. An estimated 64 tonnes of fuel was spilled in the West Wharf in Dalhousie, New Brunswick. The incident provided an opportunity to develop a response process designed for under-dock structures. The response process involved the following 3 phases: (1) survey and documentation, (2) assessment and characterization, and (3) under-dock treatment plan, development and implementation. Containment booms were deployed around the vessel and dock to control the movement of oil. Oil was also contained on the surface decking of the dock. Most of the oil was contained to the immediate area of the dock. Only a small amount of oil escaped outside the containment boom. The methodology used in this incident proved to be effective and has broader application for future spills. The development of a Dock Oiling Cleanup Assessment Technique (DOCAT) that is complimentary to the established Shoreline Cleanup Assessment Technique (SCAT) process was recommended. 2 refs., 2 tabs., 6 figs.

  15. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta

    OpenAIRE

    Zhe Zhang; Schindler, Christina E. M.; Lange, Oliver F.; Martin Zacharias

    2015-01-01

    The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamilto...

  16. Astronaut Brand and Cosmonaut Ivanchenko in Docking Module trainer

    Science.gov (United States)

    1974-01-01

    Astronaut Vance D. Brand (foreground) and Cosmonaut Aleksandr S. Ivanchenko are seated in the Docking Module trainer in bldg 35 during Apollo Soyuz Test Project (ASTP) simulation training at JSC. Brand is the command module pilot of the American ASTP prime crew. Ivanchenko is the engineer on the Soviet ASTP fourth crew (back-up). During the exercise the American ASTP crew and the Soviet ASTP crew simulated docking the Apollo and Soyuz in Earth orbit and transferring to each other's spacecraft. This view is looking from inside the Command Module into the Docking Module. The hatchway leading into the Soyuz spacecraft orbital module mock-up is in the background.

  17. Short term storage of goods in cross-docking operations

    OpenAIRE

    I F A Vis; Roodbergen, K.J.

    2004-01-01

    Cross docking is one of the options to reduce lead times and inventories and to improve customer response time in supply chains. Cross-docking centres are dynamic environments where products arrive, are regrouped, and leave the same day. In this paper we focus on the process of short-term storage of unit-Ioads in a cross-docking environment. The goal is to determine temporary storage locations for incoming unit loads such that the travel distances of the forklift trucks with these unit loads ...

  18. Design of a Docking Wall-Climbing Robot

    OpenAIRE

    Rong Liu; Ran Liang

    2013-01-01

    This paper introduces an innovative wall‐climbing robot. The robot consists of two single‐body negative pressure adsorption robots which could dock together as a mother‐robot or separate into two independent child‐robots. The child‐robots connect with each other through a docking mechanism which can not only lock solidly and unlock smoothly but which can also adjust the relative position of the two child‐robots. This design guarantees that while in dock mode the mother robot will be able to c...

  19. Protein–ligand docking with multiple flexible side chains

    OpenAIRE

    Zhao, Yong; Sanner, Michel F.

    2007-01-01

    In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For these cases, we identify the side chains to be made flexible during docking calculation by superimpo...

  20. CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys.

    Directory of Open Access Journals (Sweden)

    Qingzhen Hou

    Full Text Available Large-scale identification of native binding orientations is crucial for understanding the role of protein-protein interactions in their biological context. Measuring binding free energy is the method of choice to estimate binding strength and reveal the relevance of particular conformations in which proteins interact. In a recent study, we successfully applied coarse-grained molecular dynamics simulations to measure binding free energy for two protein complexes with similar accuracy to full-atomistic simulation, but 500-fold less time consuming. Here, we investigate the efficacy of this approach as a scoring method to identify stable binding conformations from thousands of docking decoys produced by protein docking programs. To test our method, we first applied it to calculate binding free energies of all protein conformations in a CAPRI (Critical Assessment of PRedicted Interactions benchmark dataset, which included over 19000 protein docking solutions for 15 benchmark targets. Based on the binding free energies, we ranked all docking solutions to select the near-native binding modes under the assumption that the native-solutions have lowest binding free energies. In our top 100 ranked structures, for the 'easy' targets that have many near-native conformations, we obtain a strong enrichment of acceptable or better quality structures; for the 'hard' targets without near-native decoys, our method is still able to retain structures which have native binding contacts. Moreover, in our top 10 selections, CLUB-MARTINI shows a comparable performance when compared with other state-of-the-art docking scoring functions. As a proof of concept, CLUB-MARTINI performs remarkably well for many targets and is able to pinpoint near-native binding modes in the top selections. To the best of our knowledge, this is the first time interaction free energy calculated from MD simulations have been used to rank docking solutions at a large scale.

  1. Docking and Molecular Dynamics Simulations in Potential Drugs Discovery: An Application to Influenza Virus M2 Protein

    Directory of Open Access Journals (Sweden)

    Marine E. Bozdaganyan

    2014-01-01

    Full Text Available Molecular docking is a common method for searching new potential drugs. Improvement of the results of docking can be achieved by different ways-one of them is molecular dynamics simulations of protein-ligand complexes. As a model for our research we chose M2 membrane protein from influenza virus. M2 protein is a high selective tetrameric pH-gated proton channel. It was previously shown that Omeprazole Family Compounds (OFC block the "proton pump", though we hypothesized further that they could interfere with the mechanism of fusion of the virus envelope and endosomal membrane, thereby hindering the M2 proton pump mechanism of influenza viruses. We carried out a Molecular Dynamics (MD simulation in order to predict constant of binding for OFC. We simulated M2 Protein (PDB code 3C9J in complex with its ligands: Amantadine, rimantadine as positive controls and omeprazole as putative ligand. We made use of molecular docking as well as the thermodynamic integration method to estimate binding free energies of the ligands. We demonstrate that the thermodynamic integration method predicts free energies of ligand binding better than molecular docking while embedding of M2 protein in a membrane further improves the calculated free energy values. Free energy calculations imply omeprazole as a potent anti-viral drug.

  2. Arm & Interarm Star Formation in Spiral Galaxies

    CERN Document Server

    Foyle, Kelly; Walter, Fabian; Leroy, Adam

    2010-01-01

    We investigate the relationship between spiral arms and star formation in the grand-design spirals NGC 5194 and NGC 628 and in the flocculent spiral NGC 6946. Filtered maps of near-IR (3.6 micron) emission allow us to identify "arm regions" that should correspond to regions of stellar mass density enhancements. The two grand-design spirals show a clear two-armed structure, while NGC 6946 is more complex. We examine these arm and interarm regions, looking at maps that trace recent star formation - far-ultraviolet (GALEX NGS) and 24 micron emission (Spitzer, SINGS) - and cold gas - CO (Heracles) and HI (Things). We find the star formation tracers and CO more concentrated in the spiral arms than the stellar 3.6 micron flux. If we define the spiral arms as the 25% highest pixels in the filtered 3.6 micron images, we find that the majority (60%) of star formation tracers occurs in the interarm regions; this result persists qualitatively even when considering the potential impact of finite data resolution and diffu...

  3. Adaptive control strategies for cooperative dual-arm manipulators

    Science.gov (United States)

    Seraji, H.

    1987-01-01

    Three strategies for adaptive control of cooperative dual-arm robots are discussed. Implementation of these adaptive controllers does not require the use of complex mathematical models of the arm dynamics or knowledge of the arm dynamic parameters or load parameters. These strategies have simple structures, and are computationally fast for on-line implementation with high sampling rates. In all three cases, the coupling effects between the arms through the load are treated as disturbances which are rejected by the adaptive controllers while following desired commands in a common frame of reference. Simulation results demonstrate the usefulness of the controllers.

  4. Diverse, high-quality test set for the validation of protein-ligand docking performance.

    Science.gov (United States)

    Hartshorn, Michael J; Verdonk, Marcel L; Chessari, Gianni; Brewerton, Suzanne C; Mooij, Wijnand T M; Mortenson, Paul N; Murray, Christopher W

    2007-02-22

    A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do not represent proteins thought to be of direct interest to the pharmaceutical or agrochemical industry. Rules have been used to exclude complexes containing non-drug-like ligands. One complex from each cluster has been selected where a structure of sufficient quality was available. The final Astex diverse set contains 85 diverse, relevant protein-ligand complexes, which have been prepared in a format suitable for docking and are to be made freely available to the entire research community (http://www.ccdc.cam.ac.uk). The performance of the docking program GOLD against the new set is assessed using a variety of protocols. Relatively unbiased protocols give success rates of approximately 80% for redocking into native structures, but it is possible to get success rates of over 90% with some protocols. PMID:17300160

  5. Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface.

    Science.gov (United States)

    Schadzek, Patrik; Schlingmann, Barbara; Schaarschmidt, Frank; Lindner, Julia; Koval, Michael; Heisterkamp, Alexander; Ngezahayo, Anaclet; Preller, Matthias

    2016-06-01

    The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants hCx46N188Q and hCx46N188D. Within the 50 ns simulation time the docked complex composed of the mutants dissociate while hCx46wt remains stable. The data indicates that one hCx46 molecule forms 5-7 hydrogen bonds (HBs) with the counterpart connexin of the opposing connexon. These HBs appear essential for a stable docking of the connexons as shown by the simulation of an entire gap junction channel and were lost for all the tested mutants. The data described here are related to the research article entitled "The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels" (Schadzek et al., 2015) [1]. PMID:26958636

  6. Antiviral activity of Ellagic Acid against envelope proteins from Dengue Virus through Insilico Docking

    Directory of Open Access Journals (Sweden)

    Giridharan Bupesh

    2014-06-01

    Full Text Available Arbo viral infection such as dengue, chikungunya, japanese encephalitis, west nile viruses and other flaviviruses have transmemberane envelope proteins. These proteins (glycoproteins form spike-like projections responsible for virus attachment to target cells and acid-activated membrane fusion. Further it targets numerous serologic reactions and tests including neutralization and hemagglutination inhibition. These viruses showed wide range of antigenic cross reactions and caused by seven antigenic complexes from 30 species, huge subtypes and varieties. This protein is the chief site for most neutralizing epitopes, highly conserved with cross-reactive epitopes. In the present study, the ellagic acid (4,4,5,5,6,6-Hexahydroxydiphenic acid 2,6,2,6-dilactone was evaluated for the antiviral activity through Insilico docking against drug target envelope proteins from dengue viruses. Ellagic acid showed good docking score with all the four glycoproteins from dengue 1-4 viruses. Among the glycoprotein receptors the glycoprotein-1 and 4 demonstrates the highest docking score with energy minimization. This highlights that the ellagic acid have potent antiviral activity against the dengue viruses.

  7. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results.

    Science.gov (United States)

    ten Brink, Tim; Exner, Thomas E

    2009-06-01

    In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and Recognition System). First, the most probable protonations, as defined by this rule based system, were compared to the ones stored in the well-known, manually revised CCDC/ASTEX data set. Then, to investigate the influence of the ligand protonation state on the docking results, different protonation states were created. Redocking and virtual screening experiments were conducted demonstrating that both docking programs have problems in identifying the correct protomer for each complex. Therefore, a preselection of plausible protomers or the improvement of the scoring functions concerning their ability to rank different molecules/states is needed. Additionally, ligand stereoisomers were tested for a subset of the CCDC/ASTEX set, showing similar problems regarding the ranking of these stereoisomers as the ranking of the protomers. PMID:19453150

  8. Nonspecific Arm Pain

    Directory of Open Access Journals (Sweden)

    Ali Moradi

    2013-12-01

    Full Text Available Nonspecific activity-related arm pain is characterized by an absence of objective physical findings and symptoms that do not correspond with objective pathophysiology. Arm pain without strict diagnosis is often related to activity, work-related activity in particular, and is often seen in patients with physically demanding work. Psychological factors such as catastrophic thinking, symptoms of depression, and heightened illness concern determine a substantial percentage of the disability associated with puzzling hand and arm pains. Ergonomic modifications can help to control symptoms, but optimal health may require collaborative management incorporating psychosocial and psychological elements of illness.

  9. Nonspecific Arm Pain

    Directory of Open Access Journals (Sweden)

    Ali Moradi

    2013-12-01

    Full Text Available   Nonspecific activity-related arm pain is characterized by an absence of objective physical findings and symptoms that do not correspond with objective pathophysiology. Arm pain without strict diagnosis is often related to activity, work-related activity in particular, and is often seen in patients with physically demanding work. Psychological factors such as catastrophic thinking, symptoms of depression, and heightened illness concern determine a substantial percentage of the disability associated with puzzling hand and arm pains. Ergonomic modifications can help to control symptoms, but optimal health may require collaborative management incorporating psychosocial and psychological elements of illness.

  10. Dictyostelium Dock180-related RacGEFs Regulate the Actin Cytoskeleton during Cell Motility

    OpenAIRE

    Para, Alessia; Krischke, Miriam; Merlot, Sylvain; Shen, Zhouxin; Oberholzer, Michael; Lee, Susan; Briggs, Steven; Firtel, Richard A.

    2009-01-01

    Cell motility of amoeboid cells is mediated by localized F-actin polymerization that drives the extension of membrane protrusions to promote forward movements. We show that deletion of either of two members of the Dictyostelium Dock180 family of RacGEFs, DockA and DockD, causes decreased speed of chemotaxing cells. The phenotype is enhanced in the double mutant and expression of DockA or DockD complements the reduced speed of randomly moving DockD null cells' phenotype, suggesting that DockA ...

  11. HERMES docking/berthing system pilot study. Quantitative assessment

    International Nuclear Information System (INIS)

    This study falls within the framework of the incorporation of quantitative risk assessment to the activities planned for the ESA-HERMES project (ESA/ CNES). The main objective behind the study was the analysis and evaluation of the potential contribution of so-called probabilistic or quantitative safety analysis to the optimization of the safety development process for the systems carrying out the safety functions required by the new and complex HERMES Space Vehicle. For this purpose, a pilot study was considered a good start in quantitative safety assessments (QSA), as this approach has been frequently used in the past to establish a solid base in large-scale QSA application programs while avoiding considerable economic risks. It was finally decided to select the HERMES docking/berthing system with Man Tender Free Flyer as the case-study. This report describes the different steps followed in the study, along with the main insights obtained and the general conclusions drawn from the study results. (author)

  12. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.

    Directory of Open Access Journals (Sweden)

    Zhe Zhang

    Full Text Available The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches.

  13. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.

    Science.gov (United States)

    Zhang, Zhe; Schindler, Christina E M; Lange, Oliver F; Zacharias, Martin

    2015-01-01

    The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC) was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches. PMID:26053419

  14. Geometric filters for protein–ligand complexes based on phenomenological molecular models

    OpenAIRE

    Sudakov O. O.; Balinskyi O. M.; Platonov M. O.; Kovalskyy D. B.

    2013-01-01

    Molecular docking is a widely used method of computer-aided drug design capable of accurate prediction of protein-ligand complex conformations. However, scoring functions used to estimate free energy of binding still lack accuracy. Aim. Development of computationally simple and rapid algorithms for ranking ligands based on docking results. Methods. Computational filters utilizing geometry of protein-ligand complex were designed. Efficiency of the filters was verified in a cross-docking study ...

  15. Designing coarse grained-and atom based-potentials for protein-protein docking

    Directory of Open Access Journals (Sweden)

    Tobi Dror

    2010-11-01

    Full Text Available Abstract Background Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations. Results Using a linear programming (LP technique, we developed two types of potentials: (i Side chain-based and (ii Heavy atom-based. To achieve this we considered a set of 161 transient complexes and generated a large set of putative docked structures (decoys, based on a shape complementarity criterion, for each complex. The demand on the potentials was to yield, for the native (correctly docked structure, a potential energy lower than those of any of the non-native (misdocked structures. We show that the heavy atom-based potentials were able to comply with this requirement but not the side chain-based one. Thus, despite the smaller number of parameters, the capability of heavy atom-based potentials to discriminate between native and "misdocked" conformations is improved relative to those of the side chain-based potentials. The performance of the atom-based potentials was evaluated by a jackknife test on a set of 50 complexes taken from the Zdock2.3 decoys set. Conclusions Our results show that, using the LP approach, we were able to train our potentials using a dataset of transient complexes only the newly developed potentials outperform three other known potentials in this test.

  16. 300,000-tonnage Crude Oil Dock Put into Operation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Aproject of Jointly establishing 300,000-tonnage crude oil dock of Tianjin Port has been put into operations, thanks to its outut grid successfully connected with oil pipeline of Sinopec Tanggu reservior.

  17. AggieSat: Autonomous Rendezvous and Docking Technology Demonstrator Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Current autonomous rendezvous and docking (AR&D) capability in low Earth orbit (LEO) is constrained by sensor and effector mass, power, and accuracy limits. To...

  18. Optimal Rendezvous and Docking Simulator for Elliptical Orbits Project

    Data.gov (United States)

    National Aeronautics and Space Administration — It is proposed to develop and implement a simulation of spacecraft rendezvous and docking guidance, navigation, and control in elliptical orbit. The foundation of...

  19. Collision Analysis of the Spar Upper Module Docking

    Institute of Scientific and Technical Information of China (English)

    Yan Liu; Liping Sun; Chunlin Wu; Guo Wei

    2014-01-01

    In order to assess the possible collision effect, a numerical simulation for the upper module and spar platform docking at the speed of 0.2 m/s was conducted by using the software ANSYS/LS-DYNA, and the time history of the collision force, energy absorption and structural deformation during the collision was described. The purpose was to ensure that the platform was safely put into operation. Furthermore, this paper analyzes different initial velocities and angles on the Von Mises stress and collision resultant force during the docking collision. The results of this paper showed that the docking could be conducted with higher security. The data in this paper can provide useful references for the determination of the upper module’s offshore hoisting scheme and practical construction by contrasting the numerical simulation results of the parameters on the docking collision.

  20. Molecular docking studies in factor XIa binding site

    Science.gov (United States)

    Balaji, Govardhan A.; Balaji, Vitukudi N.; Rao, Shashidhar N.

    2016-03-01

    Factor XIa inhibitors have been identified to have potential as anticoagulants with robust efficacy and low bleeding risks. In light of their significance and the availability of their 3-D X-ray data in the PDB, we present molecular docking studies carried out with a view to obtain docking protocols that will successfully reproduce the experimentally observed protein-ligand interactions in the case of various X-ray ligands. In this context, we have specifically investigated the efficacy of various cross-docking protocols in reproducing experimental data. Our studies demonstrate that an ensemble of the three apo proteins is capable of accurately docking a majority of the X-ray ligands accurately without invoking any additional conformational flexibility than that present in their experimental structures. Further, we demonstrate that such an ensemble is successfully able to enrich a collection of known active factor XIa inhibitors embedded in a decoy database of drug-like molecules.

  1. Fault-Tolerant Relative Navigation System (RNS) for Docking Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A method is propsed to develop a sensor fusion process for blending GPS/IMU/EO data for fault tolerant rendezvous and docking of spacecraft. The methodology takes...

  2. Feasibility of the SIMAC for the NASA Docking System

    Science.gov (United States)

    Motaghedi, Pejmun; Ghofranian, Siamak

    2014-01-01

    In April 2012, NASA directed Boeing to conduct a study to assess the feasibility of implementing a simplified soft capture system, as a possible replacement for the soft capture system portion of the baseline NASA Docking System (NDS). This paper describes the study conducted and conclusions drawn that supported the selection of the Soft Impact Mating and Attenuation Concept (SIMAC) as the replacement of the International Low Impact Docking System's (iLIDS) soft capture system.

  3. JUST IN SEQUENCE SUPPLY WITH MULTILEVEL CROSS DOCKING

    OpenAIRE

    ÁGOTA BÁNYAI

    2013-01-01

    The globalisation of the economy, which can be described by the reduction of transportation, communication and management costs, has changed the structure of logistics processes including purchasing, production, distribution and recycling. Production companies try to optimise their supply chain to reduce the logistics costs. One of the most powerful methods to simplify the supply chain is the cross docking. The aim of cross docking is to sort products intended for different production destina...

  4. Horizontale en verticale samenwerking in distributieketens met cross-docks

    OpenAIRE

    Buijs, Paul

    2014-01-01

    Logistiek dienstverleners staan voor grote uitdagingen op het gebied van duurzaamheid, in het bijzonder vanwege de steeds kleiner wordende zendingen die just-in-time bij de klant moeten worden afgeleverd. Samenwerking tussen partners in de distributieketen en met concurrenten daarbuiten biedt kansen om deze uitdagingen het hoofd te bieden. Dit proefschrift richt zich op samenwerkingsvormen in distributieketens met cross-docks. Cross-docks zijn logistieke centra die bedrijven in staat stellen ...

  5. Towards predictive docking at aminergic G-protein coupled receptors.

    Science.gov (United States)

    Jakubík, Jan; El-Fakahany, Esam E; Doležal, Vladimír

    2015-11-01

    G protein-coupled receptors (GPCRs) are hard to crystallize. However, attempts to predict their structure have boomed as a result of advancements in crystallographic techniques. This trend has allowed computer-aided molecular modeling of GPCRs. We analyzed the performance of four molecular modeling programs in pose evaluation of re-docked antagonists / inverse agonists to 11 original crystal structures of aminergic GPCRs using an induced fit-docking procedure. AutoDock and Glide were used for docking. AutoDock binding energy function, GlideXP, Prime MM-GB/SA, and YASARA binding function were used for pose scoring. Root mean square deviation (RMSD) of the best pose ranged from 0.09 to 1.58 Å, and median RMSD of the top 60 poses ranged from 1.47 to 3.83 Å. However, RMSD of the top pose ranged from 0.13 to 7.33 Å and ranking of the best pose ranged from the 1st to 60th out of 60 poses. Moreover, analysis of ligand-receptor interactions of top poses revealed substantial differences from interactions found in crystallographic structures. Bad ranking of top poses and discrepancies between top docked poses and crystal structures render current simple docking methods unsuitable for predictive modeling of receptor-ligand interactions. Prime MM-GB/SA optimized for 3NY9 by multiple linear regression did not work well at 3NY8 and 3NYA, structures of the same receptor with different ligands. However, 9 of 11 trajectories of molecular dynamics simulations by Desmond of top poses converged with trajectories of crystal structures. Key interactions were properly detected for all structures. This procedure also worked well for cross-docking of tested β2-adrenergic antagonists. Thus, this procedure represents a possible way to predict interactions of antagonists with aminergic GPCRs. PMID:26453085

  6. Scheduling inbound and outbound trucks at cross docking terminals

    OpenAIRE

    Nils Boysen; Malte Fliedner; Armin Scholl

    2007-01-01

    At cross docking terminals, shipments from inbound trucks are unloaded, sorted and moved to dispatch points where they are directly loaded onto outbound trucks for an immediate delivery elsewhere in the distribution system. This warehouse management concept aims at realizing economies in transportation cost by consolidating divergent shipments to full truckloads without requiring excessive inventory at the cross dock. The efficient operation of such a system requires an appropriate coordinati...

  7. A Review: Mathematical Modles for Cross Docking Planning

    OpenAIRE

    Dwi Agustina; Lee, C.K.M.; Rajesh Piplani

    2010-01-01

    This paper provides a comprehensive literature review of mathematical models in cross docking planning. From the reviews, the models are classified in three different levels regarding its decisions level which are operational, tactical, and strategic level. The researches in operational level are mainly related to develop model in scheduling, dock door assignment, transhipment problem, vehicle routing, and product allocation. For tactical and strategic level, the researches are mainly proposi...

  8. An Elastica Arm Scale

    CERN Document Server

    Bosi, F; Corso, F Dal; Bigoni, D

    2015-01-01

    The concept of 'deformable arm scale' (completely different from a traditional rigid arm balance) is theoretically introduced and experimentally validated. The idea is not intuitive, but is the result of nonlinear equilibrium kinematics of rods inducing configurational forces, so that deflection of the arms becomes necessary for the equilibrium, which would be impossible for a rigid system. In particular, the rigid arms of usual scales are replaced by a flexible elastic lamina, free of sliding in a frictionless and inclined sliding sleeve, which can reach a unique equilibrium configuration when two vertical dead loads are applied. Prototypes realized to demonstrate the feasibility of the system show a high accuracy in the measure of load within a certain range of use. It is finally shown that the presented results are strongly related to snaking of confined beams, with implications on locomotion of serpents, plumbing, and smart oil drilling.

  9. ARM7-kehityskortti

    OpenAIRE

    Kukkonen, Henri

    2006-01-01

    Tämän opinnäytetyön tarkoituksena oli suunnitella ja toteuttaa ARM-mikro-ohjain pohjainen kehityskortti. Kortin tuli olla soveltuva ARM-ohjelmoinnin opettamiseen. Työssä myös selvitettiin ARM-mikro-ohjaimen ohjelmointiympäristön käyttöönotto. Teoriaosassa käsitellään ARM-arkkitehtuuria, työssä käytettyjen Atmelin AT91R40008-mikro-ohjaimen sekä Philipsin LPC2105-mikro-ohjaimen ominaisuuksia. Erityisesti työssä keskitytään kehityskorttien suunnitteluun. Kehityskortin vaatimuksina oli, että se ...

  10. ARM for Platform Application

    Science.gov (United States)

    Patte, Mathieu; Poupat, Jean-Luc; Le Meur, Patrick

    2015-09-01

    The activities described in this paper are part of the CNES R&T “Study of a Cortex-R ARM based architecture” performed by Airbus DS Space System & Electronics in 2014. With the support of CNES, Airbus DS has performed the porting of a representative space application software on an ARM based demonstration platform. This paper presents the platform itself, the activities performed at software level and the first results on this evaluation study.

  11. Effects of administration of a local anaesthetic and/or an NSAID and of docking length on the behaviour of piglets during 5 h after tail docking

    DEFF Research Database (Denmark)

    Herskin, Mette S.; Di Giminiani, Pierpaolo; Thodberg, Karen

    2016-01-01

    In many countries, piglets are tail docked to prevent tail biting. The aim of this study was 1) to evaluate the efficacy of a local anaesthetic and/or NSAID to reduce pain caused by tail docking; and 2) to examine interactions with docking length. This was examined in 295 piglets docked by hot iron...... cautery 2–4 days after birth and based on behaviour during docking as well as the following 5 h. The study involved three main factors: local anaesthetic (Lidocain), NSAID (Meloxicam) and docking length. Either 100%, 75%, 50% or 25% of the tails were left on the body of the piglets. Irrespective of the...... tail length, tail docking led to signs of procedural pain, which could be reduced by administration of Lidocain. Preemptive use of Meloxicam did not affect the signs of procedural pain. The results show that tail docking led to behavioural changes throughout the 5 h observation period indicating that...

  12. Identification of hot-spot residues in protein-protein interactions by computational docking

    Directory of Open Access Journals (Sweden)

    Fernández-Recio Juan

    2008-10-01

    Full Text Available Abstract Background The study of protein-protein interactions is becoming increasingly important for biotechnological and therapeutic reasons. We can define two major areas therein: the structural prediction of protein-protein binding mode, and the identification of the relevant residues for the interaction (so called 'hot-spots'. These hot-spot residues have high interest since they are considered one of the possible ways of disrupting a protein-protein interaction. Unfortunately, large-scale experimental measurement of residue contribution to the binding energy, based on alanine-scanning experiments, is costly and thus data is fairly limited. Recent computational approaches for hot-spot prediction have been reported, but they usually require the structure of the complex. Results We have applied here normalized interface propensity (NIP values derived from rigid-body docking with electrostatics and desolvation scoring for the prediction of interaction hot-spots. This parameter identifies hot-spot residues on interacting proteins with predictive rates that are comparable to other existing methods (up to 80% positive predictive value, and the advantage of not requiring any prior structural knowledge of the complex. Conclusion The NIP values derived from rigid-body docking can reliably identify a number of hot-spot residues whose contribution to the interaction arises from electrostatics and desolvation effects. Our method can propose residues to guide experiments in complexes of biological or therapeutic interest, even in cases with no available 3D structure of the complex.

  13. Hello to Arms

    Science.gov (United States)

    2005-01-01

    This image highlights the hidden spiral arms (blue) that were discovered around the nearby galaxy NGC 4625 by the ultraviolet eyes of NASA's Galaxy Evolution Explorer. The image is composed of ultraviolet and visible-light data, from the Galaxy Evolution Explorer and the California Institute of Technology's Digitized Sky Survey, respectively. Near-ultraviolet light is colored green; far-ultraviolet light is colored blue; and optical light is colored red. As the image demonstrates, the lengthy spiral arms are nearly invisible when viewed in optical light while bright in ultraviolet. This is because they are bustling with hot, newborn stars that radiate primarily ultraviolet light. The youthful arms are also very long, stretching out to a distance four times the size of the galaxy's core. They are part of the largest ultraviolet galactic disk discovered so far. Located 31 million light-years away in the constellation Canes Venatici, NGC 4625 is the closest galaxy ever seen with such a young halo of arms. It is slightly smaller than our Milky Way, both in size and mass. However, the fact that this galaxy's disk is forming stars very actively suggests that it might evolve into a more massive and mature galaxy resembling our own. The armless companion galaxy seen below NGC 4625 is called NGC 4618. Astronomers do not know why it lacks arms but speculate that it may have triggered the development of arms in NGC 4625.

  14. Homology modeling and docking studies of IscS from extremophile Acidithiobacillus ferrooxidans

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The gene iscS-3 from Acidithiobacillus ferrooxidans may play a central role in the delivery of sulfur to a variety of metabolic pathways in this organism. For insight into the sulfur metabolic mechanism of the bacteria, an integral three-dimensional (3D) molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and further used to search bind sites, carry out flexible docking with cofactor pyridoxal 5'-phosphate(PLP) and substrate cysteine and hereby detect its key residues. Through these procedures, the detail conformations of PLP-IscS(P-I) and cysteine-PLP-IscS(C-P-I) complexes were obtained. In P-I complex, the residues of Lys208, His106, Thr78, Ser205, His207, Asp182 and Gln185 have large interaction energies and/or hydrogen bonds fixation with PLP. In C-P-I complex, the amino group in cysteine is very near His106, Lys208 and PLP, the interaction energies for cysteine with them are very high. The above results are well consistent with those experimental facts of the homologues from other sources. Interestingly, the four residues of Glu105, Glu79, Ser203 and His180 in P-I docking and the residue of Lys213 in C-P-I docking also have great interaction energies, which are fitly conservation in IscSs from all kinds of sources but have not been identified before. From these results, this gene can be confirmed at 3D level to encode the iron-sulfur cluster assembly protein lscS and subsequently play a sulfur traffic role. Furthermore, the substrate cysteine can be presumed to be effectively recruited into the active site. Finally, the above detected key residues can be conjectured to be directly responsible for the bind and/or catalysis of PLP and cysteine.

  15. Spectroscopy and molecular docking studies on the binding of propyl gallate to human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Guo-fei; Wang, Yu; Xi, Lei; Liu, Jin; Wang, Hao; Du, Lin-fang, E-mail: dulinfang@scu.edu.cn

    2015-03-15

    The interaction of propyl gallate (PG) with human serum albumin (HSA) was investigated by fluorescence, far-UV CD and FT-IR spectroscopic methods as well as molecular docking. Fluorescence emission spectra demonstrated that the HSA fluorescence was quenched by PG through static quenching and energy transfer with the binding constants in the order of 10{sup 5} L mol{sup −1}. The thermodynamic parameters (ΔH=−29.64 KJ mol{sup −1}, ΔS=2.7 J mol{sup −1} K{sup −1}) indicated that both hydrophobic force and hydrogen bond interactions played a leading role in the formation of PG–HSA complex. The results also showed the existence of a single binding site, which was located in subdomain IIA (site I) as revealed by molecular docking and competitive binding experiments. Molecular docking studies further showed the participation of several amino acids in PG–HSA complexation, which stabilized by H-bonding systems. The synchronous fluorescence spectra showed that the binding of drug caused the environment of tryptophan residues became more polar. FT-IR and CD spectroscopic further showed that drug complexation altered protein conformation by a major reduction of α-helix inducing a partial protein destabilization. - Highlights: • The interaction between propyl gallate and HSA has been investigated. • HSA fluorescence is quenched by propyl gallate through static quenching mechanism. • Both hydrophobic force and hydrogen bond play major role in the binding process. • Site I of the HSA is found to be the main binding site for propyl gallate. • The structure of HSA has been changed upon the interaction with propyl gallate.

  16. Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors.

    Science.gov (United States)

    Jarończyk, Małgorzata; Wołosewicz, Karol; Gabrielsen, Mari; Nowak, Gabriel; Kufareva, Irina; Mazurek, Aleksander P; Ravna, Aina W; Abagyan, Ruben; Bojarski, Andrzej J; Sylte, Ingebrigt; Chilmonczyk, Zdzisław

    2012-03-01

    It is well known that 6-nitroquipazine exhibits about 150-fold higher affinity for the serotonin transporter (SERT) than quipazine and recently we showed quipazine buspirone analogues with high to moderate SERT affinity. Now we have designed and synthesized several 6-nitroquipazine buspirone derivatives. Unexpectedly, their SERT binding affinities were moderate, and much lower than that of the previously studied quipazine buspirone analogues. To explain these findings, docking studies of both groups of compounds into two different homology models of human SERT was performed using a flexible target-ligand docking approach (4D docking). The crystal structures of leucine transporter from Aquifex aeolicus in complex with leucine and with tryptophan were used as templates for the SERT models in closed and outward-facing conformations, respectively. We found that the latter conformation represents the most reliable model for binding of buspirone analogues. Docking into that model showed that the nitrated compounds acquire a rod like shape in the binding pocket with polar groups (nitro- and imido-) at the ends of the rod. 6-Nitro substituents gave steric clashes with amino acids located at the extracellular loop 4, which may explain their lower affinity than corresponding quipazine buspirone analogues. The results from the present study may suggest chemical design strategies to improve the SERT modulators. PMID:22309909

  17. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking.

    Science.gov (United States)

    Heo, Lim; Lee, Hasup; Seok, Chaok

    2016-01-01

    Protein-protein docking methods have been widely used to gain an atomic-level understanding of protein interactions. However, docking methods that employ low-resolution energy functions are popular because of computational efficiency. Low-resolution docking tends to generate protein complex structures that are not fully optimized. GalaxyRefineComplex takes such low-resolution docking structures and refines them to improve model accuracy in terms of both interface contact and inter-protein orientation. This refinement method allows flexibility at the protein interface and in the overall docking structure to capture conformational changes that occur upon binding. Symmetric refinement is also provided for symmetric homo-complexes. This method was validated by refining models produced by available docking programs, including ZDOCK and M-ZDOCK, and was successfully applied to CAPRI targets in a blind fashion. An example of using the refinement method with an existing docking method for ligand binding mode prediction of a drug target is also presented. A web server that implements the method is freely available at http://galaxy.seoklab.org/refinecomplex. PMID:27535582

  18. Empirical scoring functions for advanced protein-ligand docking with PLANTS.

    Science.gov (United States)

    Korb, Oliver; Stützle, Thomas; Exner, Thomas E

    2009-01-01

    In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed. PMID:19125657

  19. IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking

    Science.gov (United States)

    2014-01-01

    Background Protein-protein docking is an in silico method to predict the formation of protein complexes. Due to limited computational resources, the protein-protein docking approach has been developed under the assumption of rigid docking, in which one of the two protein partners remains rigid during the protein associations and water contribution is ignored or implicitly presented. Despite obtaining a number of acceptable complex predictions, it seems to-date that most initial rigid docking algorithms still find it difficult or even fail to discriminate successfully the correct predictions from the other incorrect or false positive ones. To improve the rigid docking results, re-ranking is one of the effective methods that help re-locate the correct predictions in top high ranks, discriminating them from the other incorrect ones. In this paper, we propose a new re-ranking technique using a new energy-based scoring function, namely IFACEwat - a combined Interface Atomic Contact Energy (IFACE) and water effect. The IFACEwat aims to further improve the discrimination of the near-native structures of the initial rigid docking algorithm ZDOCK3.0.2. Unlike other re-ranking techniques, the IFACEwat explicitly implements interfacial water into the protein interfaces to account for the water-mediated contacts during the protein interactions. Results Our results showed that the IFACEwat increased both the numbers of the near-native structures and improved their ranks as compared to the initial rigid docking ZDOCK3.0.2. In fact, the IFACEwat achieved a success rate of 83.8% for Antigen/Antibody complexes, which is 10% better than ZDOCK3.0.2. As compared to another re-ranking technique ZRANK, the IFACEwat obtains success rates of 92.3% (8% better) and 90% (5% better) respectively for medium and difficult cases. When comparing with the latest published re-ranking method F2Dock, the IFACEwat performed equivalently well or even better for several Antigen/Antibody complexes

  20. Machine Vision for Relative Spacecraft Navigation During Approach to Docking

    Science.gov (United States)

    Chien, Chiun-Hong; Baker, Kenneth

    2011-01-01

    This paper describes a machine vision system for relative spacecraft navigation during the terminal phase of approach to docking that: 1) matches high contrast image features of the target vehicle, as seen by a camera that is bore-sighted to the docking adapter on the chase vehicle, to the corresponding features in a 3d model of the docking adapter on the target vehicle and 2) is robust to on-orbit lighting. An implementation is provided for the case of the Space Shuttle Orbiter docking to the International Space Station (ISS) with quantitative test results using a full scale, medium fidelity mock-up of the ISS docking adapter mounted on a 6-DOF motion platform at the NASA Marshall Spaceflight Center Flight Robotics Laboratory and qualitative test results using recorded video from the Orbiter Docking System Camera (ODSC) during multiple orbiter to ISS docking missions. The Natural Feature Image Registration (NFIR) system consists of two modules: 1) Tracking which tracks the target object from image to image and estimates the position and orientation (pose) of the docking camera relative to the target object and 2) Acquisition which recognizes the target object if it is in the docking camera Field-of-View and provides an approximate pose that is used to initialize tracking. Detected image edges are matched to the 3d model edges whose predicted location, based on the pose estimate and its first time derivative from the previous frame, is closest to the detected edge1 . Mismatches are eliminated using a rigid motion constraint. The remaining 2d image to 3d model matches are used to make a least squares estimate of the change in relative pose from the previous image to the current image. The changes in position and in attitude are used as data for two Kalman filters whose outputs are smoothed estimate of position and velocity plus attitude and attitude rate that are then used to predict the location of the 3d model features in the next image.

  1. Molecular Docking of 3-Methylindole-containing Drugs Binding into CYP3A4

    Institute of Scientific and Technical Information of China (English)

    MENG Xuan-yu; LI Zhuo; NIU Rui-juan; ZHANG Hong-xing; ZHENG Qing-chuan

    2012-01-01

    Drugs SPD-304(6,7-dimethyl-3- { [methyl-(2-{methyl-[ 1-(3-trifluoromethyl-phenyl)- 1H-indol-3-ylmethyl]-amino}-ethyl)-amino]-methyl}-chromen-4-one) and zafirlukast contain a common structural element of 3-substituted indole moiety which closely relates to a dehydrogenated reaction catalyzed by cytochrome P450s(CYPs).It was reported that the dehydrogenation can produce a reactive electrophilic intermediate which cause toxicities and inactivate CYPs. Drug L-745,870(3-{[4-(4-chlorophenyl)piperazin-l-yl]-methyl}-1H-pyrrolo-2,3-β-pyridine) might have similar effect since it contains the same structural element.We used molecular docking approach combined with molecular dynamics(MD) simulation to model three-dimensional(3D) complex structures of SPD-304,zafirlukast and L-745,870 into CYP3A4,respectively.The results show that these three drugs can stably bind into the active site and the 3-methylene carbons of the drugs keep a reasonable reactive distance from the heme iron.The complex structure of SPD-304-CYP3A4 is in agreement with experimental data.For zafirlukast,the calculation results indicate that 3-methylene carbon might be the dehydrogenation reaction site.Docking model of L-745,870-CYP3A4 shows a potential possibility of L-745,870 dehydrogenated by CYP3A4 at 3-methylene carbon which is in agreement with experiment in vivo.In addition,residues in the phenylalanine cluster as well as S119 and R212 play a critical role in the ligands binding based on our calculations.The docking models could provide some clues to understand the metabolic mechanism of the drugs by CYP3A4.

  2. Docking and molecular dynamics simulations studies of human protein kinase catalytic subunit alpha with antagonist

    Directory of Open Access Journals (Sweden)

    S. Sandeep

    2012-02-01

    Full Text Available Background: Cyclic adenosine monophosphate (cAMP dependent protein kinase A plays major role in cell signalling to undergo many cellular functions. Over expression of extracellular cAMP dependent protein kinase catalytic subunit alpha (PRKACA causes severe tumorgenesis in prostate. Thus, computer aided high throughput virtual screening and molecular dynamics simulations studies were implemented to identify the potent leads for human PRKACA.Methods: The human PRKACA crystal structure was optimized in Maestro v9.2. Fifteen recently published PRKACA inhibitors were selected for compiling 5388 structural analogs from Ligand.Info database, these were pre- pared using LigPrep. Molecular docking from lesser to higher stringency towards minor steric classes was applied subsequently to the prepared ligand dataset into PRKACA active site using Glide v5.7. Molecular dynamics simulation studies were done using Desmond v3.0 to predict the activity of PRKACA-leptosidin complex.Results: Twenty lead molecules were identified. Lead-1 was observed to have relatively the least docking score compared to the identified lead molecules and 15 published inhibitors. The PRKACA- leptosidin complex deciphered that leptosidin blocked the active site residues Thr-51, Glu-121, Val- 123, Glu-127 and Thr-183 directly through intermolecular hydrogen bonds. In molecular dynamics simulations, trajectory analysis also showed existence of water bridges between PRKACA and leptosidin.Conclusions: Docking and molecular dynamics studies revealed the better binding interaction of leptosidin with PRKACA. Leptosidin is having the better pharmacological properties thus it could be a futuristic perspective chemical compound for prostate cancer therapy.

  3. Arm To Arm Interface Using Embedded C

    Directory of Open Access Journals (Sweden)

    Mohanraj.C

    2013-02-01

    Full Text Available Embedded systems are the most emerging field in these recent years. In this paper a different number of ARM processors (LPC2148 and LPC2378 are interconnected using C for distributed services. N numbers of processors are connected as the network and each processing devices are interlinked with each other, so that the each data that is processed by the devices and it can be used by the other device to activate their entire process. All the processed data’s are communicated to other device through Xbee interface card. LPC2148 and LPC2378 ARM processors are used in this prototype and winXtalk is used as a software terminal window. In this paper, the ultimate benefits of multiple processor interactions related to the embedded applications and design issues of processor interconnection are discussed. The features of multiple processor interaction in inter process communication and executions of embedded multitasking are also discussed. In modern embedded computing platform, embedded processor used in various applications like home automation, industrial control, medical system, access control, etc. In this paper, using embedded processor interactions, the several data communication is established.

  4. GOMoDo: A GPCRs online modeling and docking webserver.

    Directory of Open Access Journals (Sweden)

    Massimo Sandal

    Full Text Available G-protein coupled receptors (GPCRs are a superfamily of cell signaling membrane proteins that include >750 members in the human genome alone. They are the largest family of drug targets. The vast diversity and relevance of GPCRs contrasts with the paucity of structures available: only 21 unique GPCR structures have been experimentally determined as of the beginning of 2013. User-friendly modeling and small molecule docking tools are thus in great demand. While both GPCR structural predictions and docking servers exist separately, with GOMoDo (GPCR Online Modeling and Docking, we provide a web server to seamlessly model GPCR structures and dock ligands to the models in a single consistent pipeline. GOMoDo can automatically perform template choice, homology modeling and either blind or information-driven docking by combining together proven, state of the art bioinformatic tools. The web server gives the user the possibility of guiding the whole procedure. The GOMoDo server is freely accessible at http://molsim.sci.univr.it/gomodo.

  5. Inspection by docking of nuclear-powered ship 'Mutsu'

    International Nuclear Information System (INIS)

    Japan Atomic Energy Research Institute carried out the docking and inspection of the nuclear-powered ship 'Mutsu' at Sekinehama Port, Mutsu City, Aomori Prefecture, from the middle of June to late in July, 1989. In this inspection, the Mutsu was mounted on a floating dock off the coast, the dock was towed by tugboats into the port and moored at the pier, and after completing the works in the dock, the dock was towed to the outside of the port, and the Mutsu was launched. The Mutsu was built as a nuclear power experiment ship, and length 130 m, breadth 19 m, depth 13.2 m, design draft at full load 6.9 m, 8242 GT. One PWR of 36 MWt and one steam turbine of 10000 ps are installed, and velocity is 16.5 knots. In September, 1974, after the first criticality, the leak of radioactivity occurred. The repair of shield and general inspection on safety were carried out in Sasebo Shipyard from August, 1980 to August, 1982. Thereafter, the Mutsu stayed in Ominato, but in January, 1988, after the completion of Sekinehama Port, the Mutsu was brought there. The Sekinehama Port, the test and inspection of the Mutsu carried out so far and the plan of hereafter are reported. (K.I.)

  6. Molecular docking assessment of pyridone derivatives as glucokinase activators

    Directory of Open Access Journals (Sweden)

    Y. Nanda Kumar

    2012-10-01

    Full Text Available Background: Mutations in glucokinase (GK gene results in maturity onset diabetes of the young 2 (MODY2. It has been observed that GK activators (GKAs can activate GK structure and promote glucose phosphorylation and bring blood glucose levels to normal condition. The present study is aimed to identify the binding mode of pyridone derivatives (PDs as GKAs through molecular docking study. Methods: GK structure was retrieved from the Protein Data Bank (PDB, protonated and energy minimized. A database was constructed with 29 PDs and docked into the allosteric site specified with Y61, R63, S69 and Y215 residues using Molecular Operating Environment (MOE software. Docking conformations were generated using triangle match algorithm and ranked by London dG scoring function. The binding orientations and strength of interactions were evaluated by ligand interaction module of MOE. Results: Molecular docking of 29 PDs in allosteric site of GK gave reliable docking scores, interestingly arene cationic interactions were observed with the compounds PD1, PD12, PD20 and PD21. R63 residue of allosteric site played a predominant role in binding with PDs. Conclusions: PDs can be potentially useful agents in future management strategies of type 2 diabetes mellitus.

  7. Granuphilin exclusively mediates functional granule docking to the plasma membrane

    Science.gov (United States)

    Mizuno, Kouichi; Fujita, Takuji; Gomi, Hiroshi; Izumi, Tetsuro

    2016-01-01

    In regulated exocytosis, it is generally assumed that vesicles must stably “dock” at the plasma membrane before they are primed to become fusion-competent. However, recent biophysical analyses in living cells that visualize fluorescent secretory granules have revealed that exocytic behaviors are not necessarily uniform: some granules beneath the plasma membrane are resistant to Ca2+ -triggered release, while others are accelerated to fuse without a pause for stable docking. These findings suggest that stable docking is unnecessary, and can even be inhibitory or nonfunctional, for fusion. Consistently, pancreatic β cells deficient in the Rab27 effector, granuphilin, lack insulin granules directly attached to the plasma membrane in electron micrographs but nevertheless exhibit augmented exocytosis. Here we directly compare the exocytic behaviors between granuphilin-positive and -negative insulin granules. Although granuphilin makes granules immobile and fusion-reluctant beneath the plasma membrane, those granuphilin-positive, docked granules release a portion of granuphilin upon fusion, and fuse at a frequency and time course similar to those of granuphilin-negative undocked granules. Furthermore, granuphilin forms a 180-nm cluster at the site of each docked granule, along with granuphilin-interacting Rab27a and Munc18-1 clusters. These findings indicate that granuphilin is an exclusive component of the functional and fusion-inhibitory docking machinery of secretory granules. PMID:27032672

  8. Children In Armed Conflicts

    OpenAIRE

    Ranjan, Tejaswini

    2013-01-01

    This is a descriptive study. A child soldier is a child under the age of 18 that is recruited into the armed forces and engages in political violence. Child Soldiers are recruited by a state or non-state armed group and used as fighters, cooks, suicide bombers, human shields, messengers, spies, or for sexual purposes. This work of research describes the plight of child soldiers taking in context the scenario of different nations. The International mechanisms to combat this problem have also b...

  9. PHENIX Muon Arms

    International Nuclear Information System (INIS)

    The PHENIX Muon Arms detect muons at rapidities of |y|=(1.2-2.4) with full azimuthal acceptance. Each muon arm must track and identify muons and provide good rejection of pions and kaons (∼10-3). In order to accomplish this we employ a radial field magnetic spectrometer with precision tracking (Muon Tracker) followed by a stack of absorber/low resolution tracking layers (Muon Identifier). The design, construction, testing and expected run parameters of both the muon tracker and the muon identifier are described

  10. PHENIX Muon Arms

    Energy Technology Data Exchange (ETDEWEB)

    Akikawa, H.; Al-Jamel, A.; Archuleta, J.B.; Archuleta, J.R.; Armendariz, R.; Armijo, V.; Awes, T.C.; Baldisseri, A.; Barker, A.B.; Barnes, P.D.; Bassalleck, B.; Batsouli, S.; Behrendt, J.; Bellaiche, F.G.; Bland, A.W.; Bobrek, M.; Boissevain, J.G.; Borel, H.; Brooks, M.L.; Brown, A.W.; Brown, D.S.; Bruner, N.; Cafferty, M.M.; Carey, T.A.; Chai, J.-S.; Chavez, L.L.; Chollet, S.; Choudhury, R.K.; Chung, M.S.; Cianciolo, V.; Clark, D.J.; Cobigo, Y.; Dabrowski, C.M.; Debraine, A.; DeMoss, J.; Dinesh, B.V.; Drachenberg, J.L.; Drapier, O.; Echave, M.A.; Efremenko, Y.V.; En' yo, H.; Fields, D.E.; Fleuret, F.; Fried, J.; Fujisawa, E.; Funahashi, H.; Gadrat, S.; Gastaldi, F.; Gee, T.F.; Glenn, A.; Gogiberidze, G.; Gonin, M.; Gosset, J.; Goto, Y.; Granier de Cassagnac, R.; Hance, R.H.; Hart, G.W.; Hayashi, N.; Held, S.; Hicks, J.S.; Hill, J.C.; Hoade, R.; Hong, B.; Hoover, A.; Horaguchi, T.; Hunter, C.T.; Hurst, D.E.; Ichihara, T.; Imai, K.; Isenhower, L.D.L. Davis; Isenhower, L.D.L. Donald; Ishihara, M.; Jang, W.Y.; Johnson, J.; Jouan, D.; Kamihara, N.; Kamyshkov, Y.; Kang, J.H.; Kapoor, S.S.; Kim, D.J.; Kim, D.-W.; Kim, G.-B.; Kinnison, W.W.; Klinksiek, S.; Kluberg, L.; Kobayashi, H.; Koehler, D.; Kotchenda, L.; Kuberg, C.H.; Kurita, K.; Kweon, M.J.; Kwon, Y.; Kyle, G.S.; LaBounty, J.J.; Lajoie, J.G.; Lee, D.M.; Lee, S.; Leitch, M.J.; Li, Z.; Liu, M.X.; Liu, X.; Liu, Y.; Lockner, E.; Lopez, J.D.; Mao, Y.; Martinez, X.B.; McCain, M.C.; McGaughey, P.L.; Mioduszewski, S.; Mischke, R.E.; Mohanty, A.K.; Montoya, B.C.; Moss, J.M.; Murata, J.; Murray, M.M.; Nagle, J.L.; Nakada, Y.; Newby, J.; Obenshain, F.; Palounek, A.P.T.; Papavassiliou, V.; Pate, S.F.; Plasil, F.; Pope, K.; Qualls, J.M.; Rao, G.; Read, K.F. E-mail: readkf@ornl.gov; Robinson, S.H.; Roche, G.; Romana, A.; Rosnet, P.; Roth, R.; Saito, N.; Sakuma, T.; Sandhoff, W.F.; Sanfratello, L.; Sato, H.D.; Savino, R.; Sekimoto, M.; Shaw, M.R.; Shibata, T.-A.; Sim, K.S.; Skank, H.D.; Smith, D.E.; Smith, G.D. [and others

    2003-03-01

    The PHENIX Muon Arms detect muons at rapidities of |y|=(1.2-2.4) with full azimuthal acceptance. Each muon arm must track and identify muons and provide good rejection of pions and kaons ({approx}10{sup -3}). In order to accomplish this we employ a radial field magnetic spectrometer with precision tracking (Muon Tracker) followed by a stack of absorber/low resolution tracking layers (Muon Identifier). The design, construction, testing and expected run parameters of both the muon tracker and the muon identifier are described.

  11. An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

    Science.gov (United States)

    Sahihi, M; Ghayeb, Y

    2014-08-01

    Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation. PMID:24880994

  12. Structural, phylogenetic and docking studies of D-amino acid oxidase activator (DAOA, a candidate schizophrenia gene

    Directory of Open Access Journals (Sweden)

    Sehgal Sheikh

    2013-01-01

    Full Text Available Abstract Background Schizophrenia is a neurodegenerative disorder that occurs worldwide and can be difficult to diagnose. It is the foremost neurological disorder leading to suicide among patients in both developed and underdeveloped countries. D-amino acid oxidase activator (DAOA, also known as G72, is directly implicated in the glutamateric hypothesis of schizophrenia. It activates D-amino acid oxidase, which oxidizes D-serine, leading to modulation of the N-methyl-D-aspartate receptor. Methods MODELLER (9v10 was utilized to generate three dimensional structures of the DAOA candidate gene. The HOPE server was used for mutational analysis. The Molecular Evolutionary Genetics Analysis (MEGA5 tool was utilized to reconstruct the evolutionary history of the candidate gene DAOA. AutoDock was used for protein-ligand docking and Gramm-X and PatchDock for protein-protein docking. Results A suitable template (1ZCA was selected by employing BLASTp on the basis of 33% query coverage, 27% identity and E-value 4.9. The Rampage evaluation tool showed 91.1% favored region, 4.9% allowed region and 4.1% outlier region in DAOA. ERRAT demonstrated that the predicted model had a 50.909% quality factor. Mutational analysis of DAOA revealed significant effects on hydrogen bonding and correct folding of the DAOA protein, which in turn affect protein conformation. Ciona was inferred as the outgroup. Tetrapods were in their appropriate clusters with bifurcations. Human amino acid sequences are conserved, with chimpanzee and gorilla showing more than 80% homology and bootstrap value based on 1000 replications. Molecular docking analysis was employed to elucidate the binding mode of the reported ligand complex for DAOA. The docking experiment demonstrated that DAOA is involved in major amino acid interactions: the residues that interact most strongly with the ligand C28H28N3O5PS2 are polar but uncharged (Gln36, Asn38, Thr 122 and non-polar hydrophobic (Ile119, Ser171

  13. Replantation (Finger, Hand, or Arm)

    Science.gov (United States)

    ... Symptom Picker Hand and Arm Conditions Carpal Tunnel Ganglion Cysts Trigger Finger Arthritis Base of the Thumb See ... Symptom Picker Hand and Arm Conditions Carpal Tunnel Ganglion Cysts Trigger Finger Arthritis Base of the Thumb See ...

  14. Modernization of African Armed Forces

    DEFF Research Database (Denmark)

    Mandrup, Thomas

    2015-01-01

    Concept paper framing the debate at the Dakar Forum Workshop on Modernization of Armed forces in Africa.......Concept paper framing the debate at the Dakar Forum Workshop on Modernization of Armed forces in Africa....

  15. Autonomous sensor-based dual-arm satellite grappling

    Science.gov (United States)

    Wilcox, Brian; Tso, Kam; Litwin, Todd; Hayati, Samad; Bon, Bruce

    1989-01-01

    Dual-arm satellite grappling involves the integration of technologies developed in the Sensing and Perception (S&P) Subsystem for object acquisition and tracking, and the Manipulator Control and Mechanization (MCM) Subsystem for dual-arm control. S&P acquires and tracks the position, orientation, velocity, and angular velocity of a slowly spinning satellite, and sends tracking data to the MCM subsystem. MCM grapples the satellite and brings it to rest, controlling the arms so that no excessive forces or torques are exerted on the satellite or arms. A 350-pound satellite mockup which can spin freely on a gimbal for several minutes, closely simulating the dynamics of a real satellite is demonstrated. The satellite mockup is fitted with a panel under which may be mounted various elements such as line replacement modules and electrical connectors that will be used to demonstrate servicing tasks once the satellite is docked. The subsystems are housed in three MicroVAX II microcomputers. The hardware of the S&P Subsystem includes CCD cameras, video digitizers, frame buffers, IMFEX (a custom pipelined video processor), a time-code generator with millisecond precision, and a MicroVAX II computer. Its software is written in Pascal and is based on a locally written vision software library. The hardware of the MCM Subsystem includes PUMA 560 robot arms, Lord force/torque sensors, two MicroVAX II computers, and unimation pneumatic parallel grippers. Its software is written in C, and is based on a robot language called RCCL. The two subsystems are described and test results on the grappling of the satellite mockup with rotational rates of up to 2 rpm are provided.

  16. Binding interaction between sorafenib and calf thymus DNA: Spectroscopic methodology, viscosity measurement and molecular docking

    Science.gov (United States)

    Shi, Jie-Hua; Chen, Jun; Wang, Jing; Zhu, Ying-Yao

    2015-02-01

    The binding interaction of sorafenib with calf thymus DNA (ct-DNA) was studied using UV-vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism (CD), viscosity measurement and molecular docking methods. The experimental results revealed that there was obvious binding interaction between sorafenib and ct-DNA. The binding constant (Kb) of sorafenib with ct-DNA was 5.6 × 103 M-1 at 298 K. The enthalpy and entropy changes (ΔH0 and ΔS0) in the binding process of sorafenib with ct-DNA were -27.66 KJ mol-1 and -21.02 J mol-1 K-1, respectively, indicating that the main binding interaction forces were van der Waals force and hydrogen bonding. The docking results suggested that sorafenib preferred to bind on the minor groove of A-T rich DNA and the binding site of sorafenib was 4 base pairs long. The conformation change of sorafenib in the sorafenib-DNA complex was obviously observed and the change was close relation with the structure of DNA, implying that the flexibility of sorafenib molecule played an important role in the formation of the stable sorafenib-ct-DNA complex.

  17. Computational Study for Protein-Protein Docking Using Global Optimization and Empirical Potentials

    Directory of Open Access Journals (Sweden)

    Kyoungrim Lee

    2008-01-01

    Full Text Available Protein-protein interactions are important for biochemical processes in biological systems. The 3D structure of the macromolecular complex resulting from the protein-protein association is a very useful source to understand its specific functions. This work focuses on computational study for protein-protein docking, where the individually crystallized structures of interacting proteins are treated as rigid, and the conformational space generated by the two interacting proteins is explored extensively. The energy function consists of intermolecular electrostatic potential, desolvation free energy represented by empirical contact potential, and simple repulsive energy terms. The conformational space is six dimensional, represented by translational vectors and rotational angles formed between two interacting proteins. The conformational sampling is carried out by the search algorithms such as simulated annealing (SA, conformational space annealing (CSA, and CSA combined with SA simulations (combined CSA/SA. Benchmark tests are performed on a set of 18 protein-protein complexes selected from various protein families to examine feasibility of these search methods coupled with the energy function above for protein docking study.

  18. ICRESH-ARMS 2015 Conference

    CERN Document Server

    Ahmadi, Alireza; Verma, Ajit; Varde, Prabhakar

    2016-01-01

    Containing selected papers from the ICRESH-ARMS 2015 conference in Lulea, Sweden, collected by editors with years of experiences in Reliability and maintenance modeling, risk assessment, and asset management, this work maximizes reader insights into the current trends in Reliability, Availability, Maintainability and Safety (RAMS) and Risk Management. Featuring a comprehensive analysis of the significance of the role of RAMS and Risk Management in the decision making process during the various phases of design, operation, maintenance, asset management and productivity in Industrial domains, these proceedings discuss key issues and challenges in the operation, maintenance and risk management of complex engineering systems and will serve as a valuable resource for those in the field.

  19. Laser space rendezvous and docking system study continuation

    Science.gov (United States)

    Adelman, S.; Heynau, H.; Levinson, S.; Weindling, F.

    1977-01-01

    Investigations were made of a configuration for a spaceborne laser radar (ladar) to meet the requirements for rendezvous and docking with a cooperative object in synchronous orbit. An analysis was completed of laser phase locking techniques, while experimental verification was made of pulse repetition frequency and resonant scanning control loops. Data measurements on a satellite mock-up were also made. The investigation supports the original contention that a rendezvous and docking ladar can be configured to offer a cost effective and reliable solution to envisioned space missions.

  20. The pickup and delivery problem with cross-docking opportunity

    DEFF Research Database (Denmark)

    Petersen, Hanne Løhmann; Røpke, Stefan

    2011-01-01

    In this paper, we consider the pickup and delivery problem with cross-docking opportunity (PDPCD). The problem arises from an industry application, and includes pickup requests, delivery requests, and pickup-and-delivery requests. Each pickup-and-delivery request can be served either as direct...... delivery by one truck, or by being picked up and transported to the cross-dock by one vehicle, and subsequently delivered at its final destination by another vehicle. Handling times at customers sites and terminal are given. A typical daily instance includes 500-1,000 requests. We solve the problem using a...

  1. Optical processing for semiautonomous terminal navigation and docking

    Science.gov (United States)

    Scholl, M. S.

    1993-01-01

    An optical cross correlator that recognizes a single object is suitable for performing a single-vision function, such as pattern recognition for semiautonomous navigation, landing, and docking of vehicles to a predesignated landing mark. The optical cross correlator, with a video input from a simple imaging system and the output of the optical correlation plane processed with standard star tracker software, produces sufficient information for a spacecraft's terminal homing navigation system to complete a docking maneuver. We describe the application of the optical cross correlator to a landing on a simulated space station.

  2. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using genetic algorithm

    Directory of Open Access Journals (Sweden)

    Ehsan Ghobadian

    2013-02-01

    Full Text Available Cross docking is one of the most important issues in management of supply chains. In cross docking, different items delivered to a warehouse by inbound trucks are directly arranged and reorganized based on customer demands, routed and loaded into outbound trucks for delivery purposes to customers without virtually keeping them at the warehouse. If any item is kept in storage, it is normally for a short amount of time, say less than 24 hours. In this paper, we consider a special case of cross docking where there is temporary storage and implements genetic algorithm to solve the resulted problem for some realistic test problems. In our method, we first use some heuristics as initial solutions and then improve the final solution using genetic algorithm. The performance of the proposed model is compared with alternative solution strategy, the GRASP method.

  3. Efficient docking of peptides to proteins without prior knowledge of the binding site

    OpenAIRE

    Hetényi, Csaba; van der Spoel, David

    2002-01-01

    Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein-protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different...

  4. A Mathematical Model for Two Dimensional Loading Problem in Cross-Docking Network Design

    OpenAIRE

    Küükoğlu, İlker; Aksoy, Aslı; Ene, Seval; ÖZTÜRK, Nursel

    2013-01-01

    In this paper, the transportation problem of cross-docking network is taken into account. Cross-docking centers differ from distribution centers or warehouses in that the loads are transported from origins to destinations through cross-docking centers without storing them for a long time. Goods are unloaded from incoming trucks and reloaded immediately onto outgoing trucks in these cross-docking centers. This problem is formulated using a mixed integer programming with two-dimensional loading...

  5. Spectroscopic and molecular docking techniques study of the interaction between oxymetholone and human serum albumin

    International Nuclear Information System (INIS)

    In this study, the binding of oxymetholone (OXM), a doping drug, to human serum albumin (HSA) was explored at pH 7.40 by spectroscopic methods including spectrofluorimetry, three dimensional excitation–emission matrix (3D EEM), UV–vis absorption, resonance rayleigh scattering (RRS) and molecular docking. The fluorescence results showed that there was a considerable quenching of the intrinsic fluorescence of HSA upon binding to OXM by static quenching mechanism. The Stern–Volmer quenching constants (KSV) between OXM and HSA at three different temperatures 295, 303, 308 K, were obtained as 4.63×104, 3.05×104 and 1.49×104 L mol−1, respectively. Furthermore this interaction was confirmed by UV–vis spectrophotometric and RRS techniques. The binding site number, n, apparent binding constant, Kb, and corresponding thermodynamic parameters (ΔS, ΔH and ΔG) were measured at different temperatures. The Van der Waals and hydrogen-bond forces were found to stabilize OXM–HSA complex. The distance (r) between the donor and acceptor was obtained from Förster's theory of fluorescence resonance energy transfer (FRET) and found to be 1.67 nm. The 3D EEM showed that OXM slightly changes the secondary structure of HSA. Furthermore, the molecular docking was employed for identification of drug binding sites and interaction of OXM with amino acid residues. - Highlights: • The binding of OXM as a doping drug with HSA was studied by different techniques. • The binding constant of HSA–OXM was calculated. • The binding site of OXM on HSA was characterized with molecular docking. • The thermodynamic parameters were calculated according to fluorescence technique

  6. MOLECULAR MODELING AND DOCKING STUDIES OF COLD ACTIVE LIPASE FROM Pseudomonas fluorescens

    Directory of Open Access Journals (Sweden)

    G. N. Gupta

    2015-03-01

    Full Text Available Molecular Modeling is essential tool in the drug design process describes the generation, manipulation or representation of 3D structures of the molecules and associated physico-chemical properties while docking predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. A cold active lipase producing potential psychrophilic bacteria (GN was isolated and identified by 16S rRNA molecular studies as Pseudomonas vancouverensis. Lipase gene from closely related species P. fluorescens was investigated for their functional role and in silico characterization using molecular modeling and docking studies. A 3D structure of lipase gene was generated with SWISS-MODEL and Discovery Studio 3.0. The stereochemistry of the constructed model of cold active lipase was subjected to energy minimization and the stereo-chemical quality of the predicted structure was assessed. The superimposition of the template (PDBID: 2Z8X with predicted structure showed that weighted root mean square deviation of Cα trace between the template and the final refined model was 0.2 Å with a significant Zscore of 8.2 and sequence identity was 80.5%. Three ligands P-Nitrophenol, Acetate ion and Diethyl phosphonate were taken for docking calculation with generated structure. They were interacting on the functional motifs of predicted model. It has been observed that Leu26, Tyr29, Asn31, Asp33, Pro315 and Thr316 residues were involved in hydrogen bonding interactions with selected ligands. So these interacted residues can be used as prominent active binding sites and which was common to the predicted active site. Based on above investigations it has been found that P. vancouverensis lipase protein can play a similar role in lipid metabolic process and triglyceride lipase functional activity as reported for P. fluorescens lipase protein.

  7. Planar Robot Arm Modelling and Control

    OpenAIRE

    Hernández González, Francisco

    2012-01-01

    The thesis objective is to model a one link robotic arm mounted on a sliding mobile platform and to investigate different control strategies under the effect of gravity and external force disturbance. For simplicity the robotic set up can be modelled and controlled as an inverted pendulum moving on a non constant sloping surface. Firstly the control is done on level ground. This lower mathematical complexity will be taken as an advantage to approach the analysis on aspects more related with c...

  8. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using GRASP method

    OpenAIRE

    Hassan Javanshir; Reza Tavakkoli-Moghaddam; Ehsan Ghobadian; Mahdi Naderi-Beni

    2012-01-01

    Cross docking play an important role in management of supply chains where items delivered to a warehouse by inbound trucks are directly sorted out, reorganized based on customer demands, routed and loaded into outbound trucks for delivery to customers without virtually keeping them at the warehouse. If any item is held in storage, it is usually for a short time, which is normally less than 24 hours. The proposed model of this paper considers a special case of cross docking where there is temp...

  9. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using genetic algorithm

    OpenAIRE

    Ehsan Ghobadian; Reza Tavakkoli-Moghaddam; Mahdi Naderi-Beni; Hassan Javanshir

    2013-01-01

    Cross docking is one of the most important issues in management of supply chains. In cross docking, different items delivered to a warehouse by inbound trucks are directly arranged and reorganized based on customer demands, routed and loaded into outbound trucks for delivery purposes to customers without virtually keeping them at the warehouse. If any item is kept in storage, it is normally for a short amount of time, say less than 24 hours. In this paper, we consider a special case of cross ...

  10. Knowledge-guided docking: Accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock

    OpenAIRE

    Cleves, AE; Jain, AN

    2015-01-01

    © 2015 The Author(s). Prediction of the bound configuration of small-molecule ligands that differ substantially from the cognate ligand of a protein co-crystal structure is much more challenging than re-docking the cognate ligand. Success rates for cross-docking in the range of 20-30 % are common. We present an approach that uses structural information known prior to a particular cutoff-date to make predictions on ligands whose bounds structures were determined later. The knowledge-guided doc...

  11. The Musculature of Coleoid Cephalopod Arms and Tentacles

    OpenAIRE

    Kier, William M.

    2016-01-01

    The regeneration of coleoid cephalopod arms and tentacles is a common occurrence, recognized since Aristotle. The complexity of the arrangement of the muscle and connective tissues of these appendages make them of great interest for research on regeneration. They lack rigid skeletal elements and consist of a three-dimensional array of muscle fibers, relying on a type of skeletal support system called a muscular hydrostat. Support and movement in the arms and tentacles depends on the fact that...

  12. The configuration space of a robotic arm in a tunnel

    OpenAIRE

    Ardila, Federico; Bastidas, Hanner; Ceballos, Cesar; Guo, John

    2016-01-01

    We study the motion of a robotic arm inside a rectangular tunnel. We prove that the configuration space of all possible positions of the robot is a CAT(0) cubical complex. This allows us to use techniques from geometric group theory to find the optimal way of moving the arm from one position to another. We also compute the diameter of the configuration space, that is, the longest distance between two positions of the robot.

  13. China Accomplished Its First Space Rendezvous and Docking

    Institute of Scientific and Technical Information of China (English)

    Chen Xiaoli

    2011-01-01

    At 1:36 am on November 3,China's Shenzhou 8 unmanned spaceship and Tiangong 1 space lab spacecraft accomplished the country's first space docking procedure and coupling in space at more than 343km above Earth's surface,marking a great leap in China's space program.

  14. Design of a Docking Wall-Climbing Robot

    Directory of Open Access Journals (Sweden)

    Rong Liu

    2013-02-01

    Full Text Available This paper introduces an innovative wall‐climbing robot. The robot consists of two single‐body negative pressure adsorption robots which could dock together as a mother‐robot or separate into two independent child‐robots. The child‐robots connect with each other through a docking mechanism which can not only lock solidly and unlock smoothly but which can also adjust the relative position of the two child‐robots. This design guarantees that while in dock mode the mother robot will be able to cross some barriers which are impossible to surmount for a single‐body wall‐climbing robot, while in separate mode the child‐robots maintain agility and mobility compared to other two‐body robots. In this paper, an overview of the mechanical structure of the robot is first presented and then three possible mechanisms for barrier‐crossing are discussed and a reasonable one is selected. An analysis of the initial docking condition of the selected design is also given which provides the basis for the experiments and research for the future.

  15. The truck scheduling problem at cross-docking terminals

    OpenAIRE

    Berghman, Lotte; Briand, Cyril; Leus, Roel; Lopez, Pierre

    2012-01-01

    We study the general case of crossdocking, in which each dock can be used both for loading and unloading (so-called mixed mode). We propose a time-indexed linear programming formulation and a branch-and- bound algorithm to solve the problem.

  16. Robot arm apparatus

    Science.gov (United States)

    Nachbar, Henry D.

    1992-01-01

    A robot arm apparatus is provided for inspecting and/or maintaining an interior of a steam generator which has an outside wall and a port for accessing the interior of the steam generator. The robot arm apparatus includes a flexible movable conduit for conveying inspection and/or maintenance apparatus from outside the steam generator to the interior of the steam generator. The flexible conduit has a terminal working end which is translated into and around the interior of the steam generator. Three motors located outside the steam generator are employed for moving the terminal working end inside the steam generator in "x", "y", and "z" directions, respectively. Commonly conducted inspection and maintenance operations include visual inspection for damaged areas, water jet lancing for cleaning sludge deposits, core boring for obtaining sludge deposits, and scrubbing of internal parts.

  17. Microelectromechanical safe arm device

    Energy Technology Data Exchange (ETDEWEB)

    Roesler, Alexander W. (Tijeras, NM)

    2012-06-05

    Microelectromechanical (MEM) apparatus and methods for operating, for preventing unintentional detonation of energetic components comprising pyrotechnic and explosive materials, such as air bag deployment systems, munitions and pyrotechnics. The MEM apparatus comprises an interrupting member that can be moved to block (interrupt) or complete (uninterrupt) an explosive train that is part of an energetic component. One or more latching members are provided that engage and prevent the movement of the interrupting member, until the one or more latching members are disengaged from the interrupting member. The MEM apparatus can be utilized as a safe and arm device (SAD) and electronic safe and arm device (ESAD) in preventing unintentional detonations. Methods for operating the MEM apparatus include independently applying drive signals to the actuators coupled to the latching members, and an actuator coupled to the interrupting member.

  18. Kiikuv maja / Anu Arm

    Index Scriptorium Estoniae

    Arm, Anu

    2006-01-01

    Eesti Kunstiakadeemia esimese kursuse arhitektuuriüliõpilaste II semestri töö. Juhendaja arhitekt Andres Alver, ehitamise Pedaspeale organiseeris suvepraktika juhendaja arhitekt Jaan Tiidemann. Autor Anu Arm, kaasa töötasid ja valmis ehitasid: Ott Alver, Maarja Elm, Mari Hunt, Alvin Järving, Marten Kaevats, Riho Kerge, Reedik Poopuu, Anu Põime, Helen Rebane, Kaisa Saarva, Martin Tago, Reet Volt. Valmis: 19. VIII 2006

  19. Tail Docking and Ear Cropping Dogs: Public Awareness and Perceptions.

    Science.gov (United States)

    Mills, Katelyn E; Robbins, Jesse; von Keyserlingk, Marina A G

    2016-01-01

    Tail docking and ear cropping are two surgical procedures commonly performed on many dog breeds. These procedures are classified as medically unnecessary surgeries whose purpose is primarily cosmetic. Available attitude research surrounding these controversial practices has been limited to surveys of veterinarians and dog breeders familiar with both practices. The aim of this project was to: 1) assess public awareness of tail docking and ear cropping, 2) determine whether physical alteration of a dog affects how the dog, and 3) owner are perceived. In Experiment 1 awareness was measured using a combination of both explicit and implicit measures. We found that 42% of participants (n = 810) were unable to correctly explain the reason why tail docked and ear cropped dogs had short ears and tails. Similarly, an implicit measure of awareness ('nature vs nurture task'), found that the majority of participants believed short tails and erect ears were a consequence of genetics rather than something the owner or breeder had done. The results obtained in Experiment 2 (n = 392) provide evidence that ear cropped and tail docked dogs are perceived differently than an identical dog in its 'natural' state. Modified dogs were perceived as being more aggressive, more dominant, less playful and less attractive than natural dogs. Experiment 3 (n = 410) is the first evidence that owners of modified dogs are perceived as being more aggressive, more narcissistic, less playful, less talkative and less warm compared to owners of natural dogs. Taken together, these results suggest that although a significant proportion of subjects appear unaware of the practices of tail docking and ear cropping in dogs, these procedures have significant impacts on how modified dogs and their owners are perceived by others. PMID:27348817

  20. Autonomous Vision-Based Tethered-Assisted Rover Docking

    Science.gov (United States)

    Tsai, Dorian; Nesnas, Issa A.D.; Zarzhitsky, Dimitri

    2013-01-01

    Many intriguing science discoveries on planetary surfaces, such as the seasonal flows on crater walls and skylight entrances to lava tubes, are at sites that are currently inaccessible to state-of-the-art rovers. The in situ exploration of such sites is likely to require a tethered platform both for mechanical support and for providing power and communication. Mother/daughter architectures have been investigated where a mother deploys a tethered daughter into extreme terrains. Deploying and retracting a tethered daughter requires undocking and re-docking of the daughter to the mother, with the latter being the challenging part. In this paper, we describe a vision-based tether-assisted algorithm for the autonomous re-docking of a daughter to its mother following an extreme terrain excursion. The algorithm uses fiducials mounted on the mother to improve the reliability and accuracy of estimating the pose of the mother relative to the daughter. The tether that is anchored by the mother helps the docking process and increases the system's tolerance to pose uncertainties by mechanically aligning the mating parts in the final docking phase. A preliminary version of the algorithm was developed and field-tested on the Axel rover in the JPL Mars Yard. The algorithm achieved an 80% success rate in 40 experiments in both firm and loose soils and starting from up to 6 m away at up to 40 deg radial angle and 20 deg relative heading. The algorithm does not rely on an initial estimate of the relative pose. The preliminary results are promising and help retire the risk associated with the autonomous docking process enabling consideration in future martian and lunar missions.

  1. Tail Docking and Ear Cropping Dogs: Public Awareness and Perceptions

    Science.gov (United States)

    Mills, Katelyn E.; Robbins, Jesse; von Keyserlingk, Marina A. G.

    2016-01-01

    Tail docking and ear cropping are two surgical procedures commonly performed on many dog breeds. These procedures are classified as medically unnecessary surgeries whose purpose is primarily cosmetic. Available attitude research surrounding these controversial practices has been limited to surveys of veterinarians and dog breeders familiar with both practices. The aim of this project was to: 1) assess public awareness of tail docking and ear cropping, 2) determine whether physical alteration of a dog affects how the dog, and 3) owner are perceived. In Experiment 1 awareness was measured using a combination of both explicit and implicit measures. We found that 42% of participants (n = 810) were unable to correctly explain the reason why tail docked and ear cropped dogs had short ears and tails. Similarly, an implicit measure of awareness (‘nature vs nurture task’), found that the majority of participants believed short tails and erect ears were a consequence of genetics rather than something the owner or breeder had done. The results obtained in Experiment 2 (n = 392) provide evidence that ear cropped and tail docked dogs are perceived differently than an identical dog in its ‘natural’ state. Modified dogs were perceived as being more aggressive, more dominant, less playful and less attractive than natural dogs. Experiment 3 (n = 410) is the first evidence that owners of modified dogs are perceived as being more aggressive, more narcissistic, less playful, less talkative and less warm compared to owners of natural dogs. Taken together, these results suggest that although a significant proportion of subjects appear unaware of the practices of tail docking and ear cropping in dogs, these procedures have significant impacts on how modified dogs and their owners are perceived by others. PMID:27348817

  2. Docking Studies of Binding of Ethambutol to the C-Terminal Domain of the Arabinosyltransferase from Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Guillermo Salgado-Moran

    2013-01-01

    Full Text Available The binding of ethambutol to the C-terminal domain of the arabinosyltransferase from Mycobacterium tuberculosis was studied. The analysis was performed using an in silico approach in order to find out, by docking calculations and energy descriptors, the conformer of Ethambutol that forms the most stable complex with the C-terminal domain of arabinosyltransferase. The complex shows that location of the Ethambutol coincides with the cocrystallization ligand position and that amino acid residues ASH1051, ASN740, ASP1052, and ARG1055 should be critical in the binding of Ethambutol to C-terminal domain EmbC.

  3. Spectrofluoremetric and molecular docking study on the interaction of bisdemethoxycurcumin with bovine β-casein nanoparticles

    International Nuclear Information System (INIS)

    The interaction of bisdemethoxycurcumin (BDMC), as one of the main active component of turmeric (Curcuma longa L.), with bovine β-casein nanoparticle, as an efficient drug carrier system, was investigated using steady-state fluorescence spectroscopy and molecular docking calculations. Results of fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations suggested that BDMC bind to the hydrophobic core of β-casein via formation of 3 hydrogen bonds and several vander Waals contacts that represented the encapsulation of BDMC in β-casein micelle nanoparticles. The binding parameters including number of substantive binding sites and the binding constants were evaluated by fluorescence quenching method. Additionally, the cytotoxicity of free BDMC and BDMC-β-casein complex in human breast cancer cell line MCF7 was evaluated in vitro. The study revealed the higher cytotoxic effects of encapsulated BDMC on MCF7 cells compared to equal dose of free BDMC. -- Highlights: • BDMC binds to the hydrophobic core of β-casein. • The effective encapsulation of BDMC in β-casein micelle nanoparticles was shown. • Enhanced cytotoxicity was observed for encapsulated BDMC in β-casein nanoparticles

  4. Function, regulation and pathological roles of the Gab/DOS docking proteins

    Directory of Open Access Journals (Sweden)

    Wöhrle Franziska U

    2009-09-01

    Full Text Available Abstract Since their discovery a little more than a decade ago, the docking proteins of the Gab/DOS family have emerged as important signalling elements in metazoans. Gab/DOS proteins integrate and amplify signals from a wide variety of sources including growth factor, cytokine and antigen receptors as well as cell adhesion molecules. They also contribute to signal diversification by channelling the information from activated receptors into signalling pathways with distinct biological functions. Recent approaches in protein biochemistry and systems biology have revealed that Gab proteins are subject to complex regulation by feed-forward and feedback phosphorylation events as well as protein-protein interactions. Thus, Gab/DOS docking proteins are at the centre of entire signalling subsystems and fulfil an important if not essential role in many physiological processes. Furthermore, aberrant signalling by Gab proteins has been increasingly linked to human diseases from various forms of neoplasia to Alzheimer's disease. In this review, we provide a detailed overview of the structure, effector functions, regulation and evolution of the Gab/DOS family. We also summarize recent findings implicating Gab proteins, in particular the Gab2 isoform, in leukaemia, solid tumours and other human diseases.

  5. Caffeine and sulfadiazine interact differently with human serum albumin: A combined fluorescence and molecular docking study

    Science.gov (United States)

    Islam, Mullah Muhaiminul; Sonu, Vikash K.; Gashnga, Pynsakhiat Miki; Moyon, N. Shaemningwar; Mitra, Sivaprasad

    2016-01-01

    The interaction and binding behavior of the well-known drug sulfadiazine (SDZ) and psychoactive stimulant caffeine (CAF) with human serum albumin (HSA) was monitored by in vitro fluorescence titration and molecular docking calculations under physiological condition. The quenching of protein fluorescence on addition of CAF is due to the formation of protein-drug complex in the ground state; whereas in case of SDZ, the experimental results were explained on the basis of sphere of action model. Although both these compounds bind preferentially in Sudlow's site 1 of the protein, the association constant is approximately two fold higher in case of SDZ (∼4.0 × 104 M-1) in comparison with CAF (∼9.3 × 102 M-1) and correlates well with physico-chemical properties like pKa and lipophilicity of the drugs. Temperature dependent fluorescence study reveals that both SDZ and CAF bind spontaneously with HSA. However, the binding of SDZ with the protein is mainly governed by the hydrophobic forces in contrast with that of CAF; where, the interaction is best explained in terms of electrostatic mechanism. Molecular docking calculation predicts the binding of these drugs in different location of sub-domain IIA in the protein structure.

  6. Spectrofluoremetric and molecular docking study on the interaction of bisdemethoxycurcumin with bovine β-casein nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Mehranfar, Fahimeh [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Bordbar, Abdol-Khalegh, E-mail: bordbar@chem.ui.ac.ir [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Keyhanfar, Mehrnaz; Behbahani, Mandana [Faculty of Advanced Sciences and Technologies, Department of Biotechnology, University of Isfahan, Isfahan, 81746-73441 (Iran, Islamic Republic of)

    2013-11-15

    The interaction of bisdemethoxycurcumin (BDMC), as one of the main active component of turmeric (Curcuma longa L.), with bovine β-casein nanoparticle, as an efficient drug carrier system, was investigated using steady-state fluorescence spectroscopy and molecular docking calculations. Results of fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations suggested that BDMC bind to the hydrophobic core of β-casein via formation of 3 hydrogen bonds and several vander Waals contacts that represented the encapsulation of BDMC in β-casein micelle nanoparticles. The binding parameters including number of substantive binding sites and the binding constants were evaluated by fluorescence quenching method. Additionally, the cytotoxicity of free BDMC and BDMC-β-casein complex in human breast cancer cell line MCF7 was evaluated in vitro. The study revealed the higher cytotoxic effects of encapsulated BDMC on MCF7 cells compared to equal dose of free BDMC. -- Highlights: • BDMC binds to the hydrophobic core of β-casein. • The effective encapsulation of BDMC in β-casein micelle nanoparticles was shown. • Enhanced cytotoxicity was observed for encapsulated BDMC in β-casein nanoparticles.

  7. Homology modeling of dopamine D2 and D3 receptors: molecular dynamics refinement and docking evaluation.

    Directory of Open Access Journals (Sweden)

    Chiara Bianca Maria Platania

    Full Text Available Dopamine (DA receptors, a class of G-protein coupled receptors (GPCRs, have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D(3 (hD(3 receptor has been recently solved. Based on the hD(3 receptor crystal structure we generated dopamine D(2 and D(3 receptor models and refined them with molecular dynamics (MD protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD(3 and hD(2L receptors was differentiated by means of MD simulations and D(3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental K(i was obtained for hD(3 and hD(2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands.

  8. Quantum Chemical and Docking Insights into Bioavailability Enhancement of Curcumin by Piperine in Pepper.

    Science.gov (United States)

    Patil, Vaishali M; Das, Sukanya; Balasubramanian, Krishnan

    2016-05-26

    We combine quantum chemical and molecular docking techniques to provide new insights into how piperine molecule in various forms of pepper enhances bioavailability of a number of drugs including curcumin in turmeric for which it increases its bioavailability by a 20-fold. We have carried out docking studies of quantum chemically optimized piperine structure binding to curcumin, CYP3A4 in cytochrome P450, p-Glycoprotein and UDP-glucuronosyltransferase (UGT), the enzyme responsible for glucuronosylation, which increases the solubility of curcumin. All of these studies establish that piperine binds to multiple sites on the enzymes and also intercalates with curcumin forming a hydrogen bonded complex with curcumin. The conjugated network of double bonds and the presence of multiple charge centers of piperine offer optimal binding sites for piperine to bind to enzymes such as UDP-GDH, UGT, and CYP3A4. Piperine competes for curcumin's intermolecular hydrogen bonding and its stacking propensity by hydrogen bonding with enolic proton of curcumin. This facilitates its metabolic transport, thereby increasing its bioavailability both through intercalation into curcumin layers through intermolecular hydrogen bonding, and by inhibiting enzymes that cause glucuronosylation of curcumin. PMID:27111639

  9. Molecular docking as a popular tool in drug design, an in silico travel

    Directory of Open Access Journals (Sweden)

    de Ruyck J

    2016-06-01

    Full Text Available Jerome de Ruyck, Guillaume Brysbaert, Ralf Blossey, Marc F Lensink University Lille, CNRS UMR8576 UGSF, Lille, FranceAbstract: New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism- or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein–protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.Keywords: structure-based drug design, protein–protein docking, quaternary structure prediction, residue interaction networks, RINs, water position

  10. Spectroscopic and docking studies of the binding of two stereoisomeric antioxidant catechins to serum albumins

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Durba; Dutta, Samrajnee; Maity, Shyam Sundar [Department of Chemistry, Presidency University, Kolkata 700 073 (India); Ghosh, Sanjib, E-mail: sanjibg@cal2.vsnl.net.in [Department of Chemistry, Presidency University, Kolkata 700 073 (India); Singha Roy, Atanu; Ghosh, Kalyan Sundar [Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302 (India); Dasgupta, Swagata, E-mail: swagata@chem.iitkgp.ernet.in [Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302 (India)

    2012-06-15

    The interactions of two stereoisomeric antioxidant flavonoids, catechin (C) and epicatechin (EC) with bovine serum albumin (BSA) and human serum albumin (HSA), have been investigated by steady state and time resolved fluorescence, phosphorescence, circular dichroism (CD), FTIR and protein-ligand docking studies. The steady-state fluorescence studies indicate a single binding site for both the ligands. FTIR spectra suggest that in both the albumins, C and EC stabilize the {alpha}-helix at the cost of a corresponding loss in the {beta}-sheet structure. CD studies have been carried out using ({+-})C, and both the epimers (+)C and (-)C. The low temperature phosphorescence and protein-ligand [(+), (-) and ({+-}) forms of C and EC] docking studies indicate that the ligands bind in the proximity of Trp 134 of BSA and Trp 214 of HSA, thereby changing their solvent accessible surface areas (ASA). Asn 158 and Glu 130 side chains are found to be within the hydrogen bonding distance from the phenolic -OH groups of C and EC in the case of BSA complex. C and EC are located within the binding pocket of sub-domain IIa of HSA. - Highlights: Black-Right-Pointing-Pointer Binding of two biologically important stereoisomeric antioxidants. Black-Right-Pointing-Pointer To find a significant role in pharmacology. Black-Right-Pointing-Pointer To find the conformational changes of the protein leading to the perturbation of Trp residues.

  11. The effect of local or general anesthesia on the physiology and behavior of tail docked pigs.

    Science.gov (United States)

    Sutherland, M A; Davis, B L; McGlone, J J

    2011-06-01

    Tail docking of pigs is a routine procedure on farms to help control tail-biting behavior; however, docking can cause pain. The objective of this research was to evaluate the effect of local or general anesthesia on the physiology (experiment 1) and behavior (experiment 2) of tail docked pigs. Pigs were allocated to one of six treatment groups: (i) sham docking (CON); (ii) docking using conventional cutting (CUT) with side-cutting pliers; (iii) CUT docking plus local anesthesia injected immediately before docking (LA); (iv) CUT docking plus short-acting local anesthesia applied topically to the tail wound (SHORT); (v) CUT docking plus long-acting anesthesia applied topically to the tail wound (LONG) and (vi) CUT docking while the pig was anesthetized with carbon dioxide gas (CO(2)). In experiment 1, blood samples were collected from pigs (10 pigs per treatment) before and 30, 60 and 120 min after docking to measure leukocyte counts and percentages and cortisol concentrations. In experiment 2, the above treatments were repeated (10 pigs per treatment); the percentage of stress vocalizations were recorded during the administration of the treatments and behavior was recorded for up to 120 min after docking or handling. All pigs were weighed before and 24 h after docking and wound healing was recorded until weaning. The neutrophil/lymphocyte ratio was greater (P pigs. At 30 min, cortisol concentrations were greater (P pigs. Cortisol concentrations did not differ (P > 0.05) between SHORT and CON pigs 30 min after docking. Cortisol concentrations did not differ (P > 0.05) among pigs given pain relief at the time of docking compared with pigs' docked without pain relief. Body weight change and wound scores did not differ (P > 0.05) among treatments. The percentage of stress vocalizations increased (P pigs in response to docking or handling. The percentage of time pigs spent lying without contact after docking tended to be greater (P = 0.06) in CUT pigs compared with all

  12. Self-adaptive differential evolution algorithm incorporating local search for protein-ligand docking

    International Nuclear Information System (INIS)

    Differential Evolution (DE) algorithm is powerful in optimization problems over several real parameters. DE depends on strategies to generate new trial solutions and the associated parameter values for searching performance. In self-adaptive DE, the automatic learning about previous evolution was used to determine the best mutation strategy and its parameter settings. By combining the self-adaptive DE and Hooke Jeeves local search, we developed a new docking method named SADock (Strategy Adaptation Dock) with the help of AutoDock4 scoring function. As the accuracy and performance of SADock was evaluated in self-docking using the Astex diverse set, the introduced SADock showed better success ratio (89%) than the success ratio (60%) of the Lamarckian genetic algorithm (LGA) of AutoDock4. The self-adapting scheme enabled our new docking method to converge fast and to be robust through the various docking problems.

  13. How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases

    DEFF Research Database (Denmark)

    Udatha, D. B. R. K. Gupta; Sugaya, Nobuyoshi; Olsson, Lisbeth; Panagiotou, Gianni

    2012-01-01

    Molecular docking is the most commonly used technique in the modern drug discovery process where computational approaches involving docking algorithms are used to dock small molecules into macromolecular target structures. Over the recent years several evaluation studies have been reported by...... independent scientists comparing the performance of the docking programs by using default 'black box' protocols supplied by the software companies. Such studies have to be considered carefully as the docking programs can be tweaked towards optimum performance by selecting the parameters suitable for the...... target of interest. In this study we address the problem of selecting an appropriate docking and scoring function combination (88 docking algorithm-scoring functions) for substrate specificity predictions for feruloyl esterases, an industrially relevant enzyme family. We also propose the 'Key Interaction...

  14. EDGA: A Population Evolution Direction-Guided Genetic Algorithm for Protein-Ligand Docking.

    Science.gov (United States)

    Guan, Boxin; Zhang, Changsheng; Ning, Jiaxu

    2016-07-01

    Protein-ligand docking can be formulated as a search algorithm associated with an accurate scoring function. However, most current search algorithms cannot show good performance in docking problems, especially for highly flexible docking. To overcome this drawback, this article presents a novel and robust optimization algorithm (EDGA) based on the Lamarckian genetic algorithm (LGA) for solving flexible protein-ligand docking problems. This method applies a population evolution direction-guided model of genetics, in which search direction evolves to the optimum solution. The method is more efficient to find the lowest energy of protein-ligand docking. We consider four search methods-a tradition genetic algorithm, LGA, SODOCK, and EDGA-and compare their performance in docking of six protein-ligand docking problems. The results show that EDGA is the most stable, reliable, and successful. PMID:26895461

  15. Prediction of binding modes and affinities of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide inhibitors to the carbonic anhydrase receptor by docking and ONIOM calculations.

    Science.gov (United States)

    Samanta, Pabitra Narayan; Das, Kalyan Kumar

    2016-01-01

    Inhibition activities of a series of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamides against the human carbonic anhydrase II (HCAII) enzyme have been explored by employing molecular docking and hybrid QM/MM methods. The docking protocol has been employed to assess the best pose of each ligand in the active site cavity of the enzyme, and probe the interactions with the amino acid residues. The docking calculations reveal that the inhibitor binds to the catalytic Zn(2+) site through the deprotonated sulfonamide nitrogen atom by making several hydrophobic and hydrogen bond interactions with the side chain residues depending on the substituted moiety. A cross-docking approach has been adopted prior to the hybrid QM/MM calculation to validate the docked poses. A correlation between the experimental dissociation constants and the docked free energies for the enzyme-inhibitor complexes has been established. Two-layered ONIOM calculations based on QM/MM approach have been performed to evaluate the binding efficacy of the inhibitors. The inhibitor potency has been predicted from the computed binding energies after taking into account of the electronic phenomena associated with enzyme-inhibitor interactions. Both the hybrid (B3LYP) and meta-hybrid (M06-2X) functionals are used for the description of the QM region. To improve the correlation between the experimental biological activity and the theoretical results, a three-layered ONIOM calculation has been carried out and verified for some of the selected inhibitors. The charge transfer stabilization energies are calculated via natural bond orbital analysis to recognize the donor-acceptor interaction in the binding pocket of the enzyme. The nature of binding between the inhibitors and HCAII active site is further analyzed from the electron density distribution maps. PMID:26619075

  16. The Discovery of Spiral Arms in the Starburst Galaxy M82

    CERN Document Server

    Mayya, Y D; Luna, A

    2005-01-01

    We report the discovery of two symmetric spiral arms in the near-infrared (NIR) images of the starburst galaxy M82. The spiral arms are recovered when an axi-symmetric exponential disk is subtracted from the NIR images. The arms emerge from the ends of the NIR bar and can be traced up to three disk scalelengths. The winding of the arms is consistent with an m=2 logarithmic spiral mode of pitch angle 14 degrees. The arms are bluer than the disk in spite of their detection on the NIR images. If the northern side of the galaxy is nearer to us, as is normally assumed, the observed sense of rotation implies trailing arms. The nearly edge-on orientation, high disk surface brightness, and the presence of a complex network of dusty filaments in the optical images, are responsible for the lack of detection of the arms in previous studies.

  17. The Mechanical Performance of Subscale Candidate Elastomer Docking Seals

    Science.gov (United States)

    Bastrzyk, Marta B.; Daniels, Christopher C.

    2010-01-01

    The National Aeronautics and Space Administration is developing a Low Impact Docking System (LIDS) for future exploration missions. The mechanism is a new state-of-the-art device for in-space assembly of structures and rendezvous of vehicles. At the interface between two pressurized modules, each with a version of the LIDS attached, a composite elastomer-metal seal assembly prevents the breathable air from escaping into the vacuum of space. Attached to the active LIDS, this seal mates against the passive LIDS during docking operation. The main interface seal assembly must exhibit low leak and outgas values, must be able to withstand various harsh space environments, must remain operational over a range of temperatures from -50 C to 75 C, and perform after numerous docking cycles. This paper presents results from a comprehensive study of the mechanical performance of four candidate subscale seal assembly designs at -50, 23, 50, and 75 C test temperatures. In particular, the force required to fully compress the seal during docking, and that which is required for separation during the undocking operation were measured. The height of subscale main interface seal bulbs, as well as the test temperature, were shown to have a significant effect on the forces the main interface seal of the LIDS may experience during docking and undocking operations. The average force values required to fully compress each of the seal assemblies were shown to increase with test temperature by approximately 50% from -50 to 75 C. Also, the required compression forces were shown to increase as the height of the seal bulb was increased. The seal design with the tallest elastomer seal bulb, which was 31% taller than that with the shortest bulb, required force values approximately 45% higher than those for the shortest bulb, independent of the test temperature. The force required to separate the seal was shown to increase with decreasing temperature after 15 hours of simulated docking. No adhesion

  18. Design of an Automatic Autonomous Mini Prone-cone Microsatellite Docking Mechanism

    Institute of Scientific and Technical Information of China (English)

    LAI Yinan; DAI Ye; TIAN Hao; ZHANG Dawei

    2010-01-01

    The capability of docking, refueling, repairing, and updating microsatellites using automatic autonomous vehicles will be of significance critical value for design and operation of several space systems in the near feature. Automatic docking capability was successfully tested by many institutions such as National Space Development Agency in Japan, European Space Agency, National Aeronautics and Space Administration in USA, etc. However, there is still much more space for improvement of degree of automation during the process of docking with large deviations of the initial attitude. A novel automatic autonomous probe-cone docking mechanism used for microsatellite docking is proposed. This docking mechanism is designed according to the design indices such as miniaturization, degree of automation and automatic capture capability within large deviation of the initial attitude. On the basis of the virtual work principle, the dynamics modeling of the docking process is presented. The position of the contact point is then analyzed. Comprehensive system level simulation is conducted in the 13 kinds of typical operating conditions with the initial deviations. Capture performance is analyzed. The simulation results show that the docking mechanism can be smoothly captured within 2 s in all cases of large attitude deviation between the active and passive spacecrafts. A virtual prototype model of the docking mechanism is established through ADAMS for further verifying the correctness of the buffer parameter model and the autonomous docking capability. A laboratory platform is designed for on-the-ground experimental validation of the property of mini probe-cone docking mechanism. Repeated docking tests prove the proposed design of the mini probe-cone docking mechanism system for its high reliability, and automatic capture capability within large attitude range. The kinetic model of the docking capture process and the mechanism structure could provide some References for similar

  19. Disarmament and arms control

    International Nuclear Information System (INIS)

    This report discusses how far science and technology can provide methods of making arms control and disarmament agreements more controlable in an objective way. Two case studies have been considered, the test ban treaty and the verification of the number of strategic nuclear weapons. These lead to the conclusion that both science and politics are closely interwoven and that within what appear to be scientific arguments, political positions are being defended. Consequently scientists and technologists and the contexts in which they work, play a prominent role. (C.F.)

  20. Removable molar power arm

    OpenAIRE

    2013-01-01

    Attachment of force elements from the gingival hook of maxillary molar tubes during the retraction of the anterior teeth is very common in orthodontic practice. As the line of force passes below the center of resistance (CR) of molar, it results its mesial tipping and also anchorage loss. To overcome this problem, the line of force should pass along the CR of molar. This article highlights a method to overcome this problem by attaching a removable power arm to the headgear tube of molar tube ...

  1. Molecular docking of Glycine max and Medicago truncatula ureases with urea; bioinformatics approaches.

    Science.gov (United States)

    Filiz, Ertugrul; Vatansever, Recep; Ozyigit, Ibrahim Ilker

    2016-03-01

    Urease (EC 3.5.1.5) is a nickel-dependent metalloenzyme catalyzing the hydrolysis of urea into ammonia and carbon dioxide. It is present in many bacteria, fungi, yeasts and plants. Most species, with few exceptions, use nickel metalloenzyme urease to hydrolyze urea, which is one of the commonly used nitrogen fertilizer in plant growth thus its enzymatic hydrolysis possesses vital importance in agricultural practices. Considering the essentiality and importance of urea and urease activity in most plants, this study aimed to comparatively investigate the ureases of two important legume species such as Glycine max (soybean) and Medicago truncatula (barrel medic) from Fabaceae family. With additional plant species, primary and secondary structures of 37 plant ureases were comparatively analyzed using various bioinformatics tools. A structure based phylogeny was constructed using predicted 3D models of G. max and M. truncatula, whose crystallographic structures are not available, along with three additional solved urease structures from Canavalia ensiformis (PDB: 4GY7), Bacillus pasteurii (PDB: 4UBP) and Klebsiella aerogenes (PDB: 1FWJ). In addition, urease structures of these species were docked with urea to analyze the binding affinities, interacting amino acids and atom distances in urease-urea complexes. Furthermore, mutable amino acids which could potentially affect the protein active site, stability and flexibility as well as overall protein stability were analyzed in urease structures of G. max and M. truncatula. Plant ureases demonstrated similar physico-chemical properties with 833-878 amino acid residues and 89.39-90.91 kDa molecular weight with mainly acidic (5.15-6.10 pI) nature. Four protein domain structures such as urease gamma, urease beta, urease alpha and amidohydro 1 characterized the plant ureases. Secondary structure of plant ureases also demonstrated conserved protein architecture, with predominantly α-helix and random coil structures. In

  2. ARM AND INTERARM STAR FORMATION IN SPIRAL GALAXIES

    International Nuclear Information System (INIS)

    We investigate the relationship between spiral arms and star formation in the grand-design spirals NGC 5194 and NGC 628 and in the flocculent spiral NGC 6946. Filtered maps of near-IR (3.6 μm) emission allow us to identify 'arm regions' that should correspond to regions of stellar mass density enhancements. The two grand-design spirals show a clear two-armed structure, while NGC 6946 is more complex. We examine these arm and interarm regions, looking at maps that trace recent star formation-far-ultraviolet (GALEX NGS) and 24 μm emission (Spitzer SINGS)-and cold gas-CO (HERACLES) and H I (THINGS). We find the star formation tracers and CO more concentrated in the spiral arms than the stellar 3.6 μm flux. If we define the spiral arms as the 25% highest pixels in the filtered 3.6 μm images, we find that the majority (60%) of star formation tracers occur in the interarm regions; this result persists qualitatively even when considering the potential impact of finite data resolution and diffuse interarm 24 μm emission. Even with a generous definition of the arms (45% highest pixels), interarm regions still contribute at least 30% to the integrated star formation rate (SFR) tracers. We look for evidence that spiral arms trigger star or cloud formation using the ratios of SFR (traced by a combination of FUV and 24 μm emission) to H2 (traced by CO) and H2 to H I. Any enhancement of SFR/M(H2) in the arm region is very small (less than 10%) and the grand-design spirals show no enhancement compared to the flocculent target. Arm regions do show a weak enhancement in H2/H I compared to the interarm regions, but at a fixed gas surface density there is little clear enhancement in the H2/H I ratio in the arm regions. Thus, it seems that spiral arms may only act to concentrate the gas to higher densities in the arms.

  3. Beyond arms control? Looking for the lost paradigm.

    International Nuclear Information System (INIS)

    Since the tragic events of September 11, 2001, the international relations have become more complex and the arms control concept, born during the cold war and implemented during the 3 last decades is today marking time. Disarmament and non-proliferation, which were the keystones of arms control and international negotiations, are today undergoing erosion. This article analyzes the change of situation between the end of the 20. century and the beginning of the 21. century. Three steps are defined by the author: a 'flux' step with the signature of a huge number of international agreements about non-proliferation and arms control, a stagnation step marked by the difficulties of implementing some of the existing treaties and by the violation by some states of some of them, and a 'reflux' step marked by a freezing up of the bilateral US-Russian disarmament process and a general renouncement of the multilateral arms control concept. (J.S.)

  4. Next-generation site-directed transgenesis in the malaria vector mosquito Anopheles gambiae: self-docking strains expressing germline-specific phiC31 integrase.

    Directory of Open Access Journals (Sweden)

    Janet M Meredith

    Full Text Available Diseases transmitted by mosquitoes have a devastating impact on global health and the situation is complicated due to difficulties with both existing control measures and the impact of climate change. Genetically modified mosquitoes that are refractory to disease transmission are seen as having great potential in the delivery of novel control strategies. The Streptomyces phage phiC31 integrase system has been successfully adapted for site-directed transgene integration in a range of insects, thus overcoming many limitations due to size constraints and random integration associated with transposon-mediated transformation. Using this technology, we previously published the first site-directed transformation of Anopheles gambiae, the principal vector of human malaria. Mosquitoes were initially engineered to incorporate the phiC31 docking site at a defined genomic location. A second phase of genetic modification then achieved site-directed integration of an anti-malarial effector gene. In the current publication we report improved efficiency and utility of the phiC31 integrase system following the generation of Anopheles gambiae self-docking strains. Four independent strains, with docking sites at known locations on three different chromosome arms, were engineered to express integrase under control of the regulatory regions of the nanos gene from Anopheles gambiae. The resulting protein accumulates in the posterior oocyte to provide integrase activity at the site of germline development. Two self-docking strains, exhibiting significantly different levels of integrase expression, were assessed for site-directed transgene integration and found to demonstrate greatly improved survival and efficiency of transformation. In the fight against malaria, it is imperative to establish a broad repertoire of both anti-malarial effector genes and tissue-specific promoters to regulate their expression, enabling those offering maximum effect with minimum fitness

  5. Experimental validation of docking and capture using space robotics testbeds

    Science.gov (United States)

    Spofford, John; Schmitz, Eric; Hoff, William

    1991-01-01

    This presentation describes the application of robotic and computer vision systems to validate docking and capture operations for space cargo transfer vehicles. Three applications are discussed: (1) air bearing systems in two dimensions that yield high quality free-flying, flexible, and contact dynamics; (2) validation of docking mechanisms with misalignment and target dynamics; and (3) computer vision technology for target location and real-time tracking. All the testbeds are supported by a network of engineering workstations for dynamic and controls analyses. Dynamic simulation of multibody rigid and elastic systems are performed with the TREETOPS code. MATRIXx/System-Build and PRO-MATLAB/Simulab are the tools for control design and analysis using classical and modern techniques such as H-infinity and LQG/LTR. SANDY is a general design tool to optimize numerically a multivariable robust compensator with a user-defined structure. Mathematica and Macsyma are used to derive symbolically dynamic and kinematic equations.

  6. An electromechanical attenuator/actuator for Space Station docking

    Science.gov (United States)

    Stokes, Lebarian; Glenn, Dean; Carroll, Monty B.

    1987-01-01

    The development of a docking system for aerospace vehicles has identified the need for reusable and variably controlled attenuators/actuators for energy absorption and compliance. One approach to providing both the attenuator and the actuator functions is by way of an electromechanical attenuator/actuator (EMAA) as opposed to a hydraulic system. The use of the electromechanical devices is considered to be more suitable for a space environment because of the absence of contamination from hydraulic fluid leaks and because of the cost effectiveness of maintenance. A smart EMAA that uses range/rate/attitude sensor information to preadjust a docking interface to eliminate misalignments and to minimize contact and stroking forces is described. A prototype EMAA was fabricated and is being tested and evaluated. Results of preliminary testing and analysis already performed have established confidence that this concept is feasible and will provide the desired reliability and low maintenance for repetitive long term operation typical of Space Station requirements.

  7. X-Armed Bandits

    CERN Document Server

    Bubeck, Sébastien; Stoltz, Gilles; Szepesvari, Csaba

    2010-01-01

    We consider a generalization of stochastic bandits where the set of arms, $\\cX$, is allowed to be a generic measurable space and the mean-payoff function is "locally Lipschitz" with respect to a dissimilarity function that is known to the decision maker. Under this condition we construct an arm selection policy, called HOO hierarchical optimistic optimization), with improved regret bounds compared to previous results for a large class of problems. In particular, our results imply that if $\\cX$ is the unit hypercube in a Euclidean space and the mean-payoff function has a finite number of global maxima around which the behavior of the function is locally H\\"older continuous with a known exponent, then the expected of HOO regret is bounded up to a logarithmic factor by $\\sqrt{n}$, i.e., the rate of growth of the regret is independent of the dimension of the space. We also prove the minimax optimality of our algorithm when the dissimilarity is a metric.

  8. Homology Modeling and Molecular Docking for the Science Curriculum

    OpenAIRE

    Owen M. McDougal; Comia, Nic; Sambasivarao, S.V.; Remm, Andrew; Mallory, Chris; Oxford, Julia Thom; Maupin, C. Mark; Andersen, Tim

    2013-01-01

    DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that simplifies the exploration of computational biochemistry. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular structure creation, ligand binding calculations, and visualization of docking results. A student procedure is provided that illustrates use of DockoMatic to create a homology model for the amino propeptide regi...

  9. Griffin Technology RoadDock PSP固定带

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    长途旅行的车程中,用PSP看部电影打发时光已经成为很多人必做的事。只是PSP在车上找不到合适的固定点,从而让你的手累得慌。Griffin Technology推出的RoadDock PSP固定带就专为此设计。

  10. Freight Distribution Systems with Cross Docking: A Multidisciplinary Analysis

    OpenAIRE

    Gonzalez-Feliu, Jesus

    2012-01-01

    Freight transport assures a vital link between suppliers and customers and it represents a major source of employment. Multi-echelon distribution is one of the most common strategies in this field. This paper presents the main concepts of multi-echelon distribution with cross-docking through a multidisciplinary analysis that includes an optimization study and an interview-based analysis. The optimization analysis uses both a geographic approach based on the concept of accessibility and a scen...

  11. Freight distribution systems with cross-docking: a multidisciplinary analysis

    OpenAIRE

    Gonzalez-Feliu, Jesus

    2012-01-01

    Freight transport constitutes one of the main activities that influences economy and society, as it assures a vital link between suppliers and customers and it represents a major source of employment. Multi-echelon distribution is one of the most common strategies adopted by the transport companies in an aim of cost reduction. This paper presents the main concepts of multi-echelon distribution with cross-docks through a multidisciplinary analysis that includes an optimisation study (using bot...

  12. Towards predictive docking at aminergic G-protein coupled receptors

    Czech Academy of Sciences Publication Activity Database

    Jakubík, Jan; El-Fakahany, E. E.; Doležal, Vladimír

    2015-01-01

    Roč. 21, č. 11 (2015), s. 284. ISSN 1610-2940 R&D Projects: GA ČR(CZ) GBP304/12/G069; GA ČR(CZ) GA14-05696S; GA ČR(CZ) GA305/09/0681 Institutional support: RVO:67985823 Keywords : induced-fit docking * pose scoring * molecular dynamics * ligand-receptor interaction Subject RIV: FH - Neurology Impact factor: 1.736, year: 2014

  13. HAVS and HAV-nots: Investigating Resonance in the Human Arm Caused by Contact with Machinery

    OpenAIRE

    Viktorova, Irina; Fleck, Matthew; Kose, Muhammed

    2016-01-01

    Mechanical vibration is a vast field composed of thousands of studies and experiments regarding individual systems and structures' vibrations and oscillations. In this paper a special and complex case regarding hand-arm vibration will be studied and analyzed mathematically. The human hand-arm system is affected by vibrations caused by contact with vibrating objects. In order to understand the effect on the hand-arm system, a mathematical model of the system as two viscoelastic rods connected ...

  14. Global Positioning System Synchronized Active Light Autonomous Docking System

    Science.gov (United States)

    Howard, Richard T. (Inventor); Book, Michael L. (Inventor); Bryan, Thomas C. (Inventor); Bell, Joseph L. (Inventor)

    1996-01-01

    A Global Positioning System Synchronized Active Light Autonomous Docking System (GPSSALADS) for automatically docking a chase vehicle with a target vehicle comprising at least one active light emitting target which is operatively attached to the target vehicle. The target includes a three-dimensional array of concomitantly flashing lights which flash at a controlled common frequency. The GPSSALADS further comprises a visual tracking sensor operatively attached to the chase vehicle for detecting and tracking the target vehicle. Its performance is synchronized with the flash frequency of the lights by a synchronization means which is comprised of first and second internal clocks operatively connected to the active light target and visual tracking sensor, respectively, for providing timing control signals thereto, respectively. The synchronization means further includes first and second Global Positioning System receivers operatively connected to the first and second internal clocks, respectively, for repeatedly providing simultaneous synchronization pulses to the internal clocks, respectively. In addition, the GPSSALADS includes a docking process controller means which is operatively attached to the chase vehicle and is responsive to the visual tracking sensor for producing commands for the guidance and propulsion system of the chase vehicle.

  15. Performance of Subscale Docking Seals Under Simulated Temperature Conditions

    Science.gov (United States)

    Smith, Ian M.; Daniels, Christopher C.

    2008-01-01

    A universal docking system is being developed by the National Aeronautics and Space Administration (NASA) to support future space exploration missions to low Earth orbit (LEO), to the moon, and to Mars. The candidate docking seals for the system are a composite design consisting of elastomer seal bulbs molded into the front and rear sides of a metal ring. The test specimens were subscale seals with two different elastomer cross-sections and a 12-in. outside diameter. The seal assemblies were mated in elastomer seal-on-metal plate and elastomer seal-on-elastomer seal configurations. The seals were manufactured from S0383-70 silicone elastomer compound. Nominal and off-nominal joint configurations were examined. Both the compression load required to mate the seals and the leak rate observed were recorded while the assemblies were subjected to representative docking system operating temperatures of -58, 73, and 122 F (-50, 23, and 50 C). Both the loads required to fully compress the seals and their leak rates were directly proportional to the test temperature.

  16. Spectroscopic and Docking Studies on the Binding of Liquiritigenin with Hyaluronidase for Antiallergic Mechanism

    Science.gov (United States)

    Zeng, Hua-jin; Yang, Ran; You, Jing; Qu, Ling-bo; Sun, Yan-jun

    2016-01-01

    The inhibitory effect of liquiritigenin on hyaluronidase and its binding mechanism were investigated systematically by UV-vis absorption, fluorescence, and molecular modeling approaches. These results indicated that liquiritigenin could interact with hyaluronidase to form a liquiritigenin-hyaluronidase complex. The binding constant, number of binding sites, and thermodynamic parameters were calculated, which indicated that liquiritigenin could spontaneously bind with hyaluronidase mainly through electrostatic and hydrophobic interactions with one binding site. Synchronous fluorescence, three-dimensional fluorescence, and molecular docking results revealed that liquiritigenin bound directly to the enzyme cavity site and this binding influenced the microenvironment of the hyaluronidase activity site, resulting in reduced hyaluronidase activity. The present study provides useful information for clinical applications of liquiritigenin as a hyaluronidase inhibitor. PMID:27313960

  17. Molecular docking as a popular tool in drug design, an in silico travel

    Science.gov (United States)

    de Ruyck, Jerome; Brysbaert, Guillaume; Blossey, Ralf; Lensink, Marc F

    2016-01-01

    New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism-or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents’ synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein–protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery. PMID:27390530

  18. Robust Design of Docking Hoop for Recovery of Autonomous Underwater Vehicle with Experimental Results

    Directory of Open Access Journals (Sweden)

    Wei Peng Lin

    2015-12-01

    Full Text Available Control systems prototyping is usually constrained by model complexity, embedded system configurations, and interface testing. The proposed control system prototyping of a remotely-operated vehicle (ROV with a docking hoop (DH to recover an autonomous underwater vehicle (AUV named AUVDH using a combination of software tools allows the prototyping process to be unified. This process provides systematic design from mechanical, hydrodynamics, dynamics modelling, control system design, and simulation to testing in water. As shown in a three-dimensional simulation of an AUVDH model using MATLAB™/Simulink™ during the launch and recovery process, the control simulation of a sliding mode controller is able to control the positions and velocities under the external wave, current, and tether forces. In the water test using the proposed Python-based GUI platform, it shows that the AUVDH is capable to perform station-keeping under the external disturbances.

  19. Magic - Marine Arm Gpci Investigation of Clouds

    Science.gov (United States)

    Lewis, E. R.; Wiscombe, W. J.; Albrecht, B. A.; Bland, G.; Flagg, C. N.; Klein, S. A.; Kollias, P.; Mace, G. G.; Reynolds, M.; Schwartz, S. E.; Siebesma, P.; Teixeira, J.; Wood, R.; Zhang, M.

    2012-12-01

    MAGIC, the Marine ARM (Atmospheric Radiation Measurement program) GPCI Investigation of Clouds, will deploy the Second ARM Mobile Facility (AMF2) aboard the Horizon Lines cargo container ship M/V Spirit traversing the route between Los Angeles, CA and Honolulu, HI from October, 2012 through September, 2013 (except from a few months in the middle of this time period when the ship will be in dry dock). During this time AMF2 will observe and characterize the properties of clouds and precipitation, aerosols, and atmospheric radiation; standard meteorological and oceanographic variables; and atmospheric structure. There will also be Intensive Observational Periods (IOPs), one in January, 2013 and one in July, 2013 during which more detailed measurements of the atmospheric structure will be made. Clouds remain a major source of uncertainty in climate projections. In this context, subtropical marine boundary layer (MBL) clouds play a key role in cloud-climate feedbacks that are not well understood yet play a large role in biases both in seasonal coupled model forecasts and annual mean climate forecasts. In particular, current climate models do not accurately represent the transition from the stratocumulus (Sc) regime, with its high albedo and large impact on the global radiative balance of Earth, to shallow trade-wind cumulus (Cu), which play a fundamental role in global surface evaporation and also albedo. Climate models do not yet adequately parameterize the small-scale physical processes associated with turbulence, convection, and radiation in these clouds. Part of this inability results from lack of accurate data on these clouds and the conditions responsible for their properties, including aerosol properties, radiation, and atmospheric and oceanographic conditions. The primary objectives of MAGIC are to improve the representation of the Sc-to-Cu transition in climate models by characterizing the essential properties of this transition, and to produce the observed

  20. Small Molecule Docking from Theoretical Structural Models

    Science.gov (United States)

    Novoa, Eva Maria; de Pouplana, Lluis Ribas; Orozco, Modesto

    Structural approaches to rational drug design rely on the basic assumption that pharmacological activity requires, as necessary but not sufficient condition, the binding of a drug to one or several cellular targets, proteins in most cases. The traditional paradigm assumes that drugs that interact only with a single cellular target are specific and accordingly have little secondary effects, while promiscuous molecules are more likely to generate undesirable side effects. However, current examples indicate that often efficient drugs are able to interact with several biological targets [1] and in fact some dirty drugs, such as chlorpromazine, dextromethorphan, and ibogaine exhibit desired pharmacological properties [2]. These considerations highlight the tremendous difficulty of designing small molecules that both have satisfactory ADME properties and the ability of interacting with a limited set of target proteins with a high affinity, avoiding at the same time undesirable interactions with other proteins. In this complex and challenging scenario, computer simulations emerge as the basic tool to guide medicinal chemists during the drug discovery process.

  1. Scheduling trucks in cross docking systems with temporary storage and dock repeat truck holding pattern using GRASP method

    Directory of Open Access Journals (Sweden)

    Hassan Javanshir

    2012-10-01

    Full Text Available Cross docking play an important role in management of supply chains where items delivered to a warehouse by inbound trucks are directly sorted out, reorganized based on customer demands, routed and loaded into outbound trucks for delivery to customers without virtually keeping them at the warehouse. If any item is held in storage, it is usually for a short time, which is normally less than 24 hours. The proposed model of this paper considers a special case of cross docking where there is temporary storage and uses GRASP technique to solve the resulted problem for some realistic test problems. In our method, we first use some heuristics as initial solutions and then improve the final solution using GRASP method. The preliminary test results indicate that the GRASP method performs better than alternative solution strategies.

  2. LISA Long-Arm Interferometry

    Science.gov (United States)

    Thorpe, James I.

    2009-01-01

    An overview of LISA Long-Arm Interferometry is presented. The contents include: 1) LISA Interferometry; 2) Constellation Design; 3) Telescope Design; 4) Constellation Acquisition; 5) Mechanisms; 6) Optical Bench Design; 7) Phase Measurement Subsystem; 8) Phasemeter Demonstration; 9) Time Delay Interferometry; 10) TDI Limitations; 11) Active Frequency Stabilization; 12) Spacecraft Level Stabilization; 13) Arm-Locking; and 14) Embarassment of Riches.

  3. Post-docking optimization and analysis of protein-ligand interactions of estrogen receptor alpha using AMMOS software.

    Science.gov (United States)

    Pencheva, Tania; Jereva, Dessislava; Miteva, Maria A; Pajeva, Ilza

    2013-03-01

    Understanding protein-ligand interactions is a critical step in rational drug design/virtual ligand screening. In this work we applied the AMMOS_ProtLig software for post-docking optimization of estrogen receptor alpha complexes generated after virtual ligand screening protocol. Using MOE software we identified the ligand-receptor interactions in the optimized complexes at different levels of protein flexibility and compared them to the experimentally observed interactions. We analyzed in details the binding sites of three X-ray complexes of the same receptor and identified the key residues for the protein-ligand interactions. The complexes were further processed with AMMOS_ProtLig and the interactions in the predicted poses were compared to those observed in the X-ray structures. The effect of employing different levels of flexibility was analyzed. The results confirmed the AMMOS_ProtLig applicability as a helpful postdocking optimization tool for virtual ligand screening of estrogen receptors. PMID:23106778

  4. Synthesis, characterization, biological activity, molecular modeling and docking studies of complexes 4-(4-hydroxy)-3-(2-pyrazine-2-carbonyl)hydrazonomethylphenyl-diazen-yl-benzenesulfonamide with manganese(II), cobalt(II), nickel(II), zinc(II) and cadmium(II)

    Science.gov (United States)

    Alaghaz, Abdel-Nasser M. A.; Zayed, Mohamed E.; Alharbi, Suliman A.; Ammar, Reda A. A.; Elhenawy, Ahmed

    2015-03-01

    A new series of complexes of 4-(4-hydroxy)-3-(2-pyrazine-2-carbonyl)hydrazonomethylphenyl-diazen-yl-benzenesulfonamide (HL) with Mn(II), Co(II), Ni(II), Zn(II) and Cd(II) have been prepared and characterized by different physical techniques. The IR spectra of the prepared complexes were suggested that the ligand behaves as a tri-dentate ligand through the carbonyl oxygen, azomethine nitrogen and phenolic oxygen atoms (ONO). Electronic spectra and magnetic susceptibility measurements reveal octahedral geometry for all complexes. The elemental analyses and mass spectral data have justified the ML2 composition of complexes. The EPR spectra of Mn(II), Co(II) and Ni(II) complexes support the mononuclear structure. The crystal field splitting, Racah repulsion and nephelauxetic parameters and determined from the electronic spectra of the complexes. Thermal properties and decomposition kinetics of all complexes are investigated. The geometry of the metal complexes has been optimized with the help of molecular modeling. The biological activity of these compounds against various fungi has been investigated.

  5. Exploring the conformational and binding properties of unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 through docking and molecular dynamics simulations.

    Science.gov (United States)

    Zacarías-Lara, Oscar J; Correa-Basurto, José; Bello, Martiniano

    2016-07-01

    B-cell lymphoma (Bcl-2) is commonly associated with the progression and preservation of cancer and certain lymphomas; therefore, it is considered as a biological target against cancer. Nevertheless, evidence of all its structural binding sites has been hidden because of the lack of a complete Bcl-2 model, given the presence of a flexible loop domain (FLD), which is responsible for its complex behavior. FLD region has been implicated in phosphorylation, homotrimerization, and heterodimerization associated with Bcl-2 antiapoptotic function. In this contribution, homology modeling, molecular dynamics (MD) simulations in the microsecond (µs) time-scale and docking calculations were combined to explore the conformational complexity of unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 systems. Conformational ensembles generated through MD simulations allowed for identifying the most populated unphosphorylated/phosphorylated monomeric conformations, which were used as starting models to obtain trimeric complexes through protein-protein docking calculations, also submitted to µs MD simulations. Principal component analysis showed that FLD represents the main contributor to total Bcl-2 mobility, and is affected by phosphorylation and oligomerization. Subsequently, based on the most representative unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 conformations, docking studies were initiated to identify the ligand binding site of several known Bcl-2 inhibitors to explain their influence in homo-complex formation and phosphorylation. Docking studies showed that the different conformational states experienced by FLD, such as phosphorylation and oligomerization, play an essential role in the ability to make homo and hetero-complexes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 393-413, 2016. PMID:27016043

  6. Finding a Potential Dipeptidyl Peptidase-4 (DPP-4) Inhibitor for Type-2 Diabetes Treatment Based on Molecular Docking, Pharmacophore Generation, and Molecular Dynamics Simulation.

    Science.gov (United States)

    Meduru, Harika; Wang, Yeng-Tseng; Tsai, Jeffrey J P; Chen, Yu-Ching

    2016-01-01

    Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme that is responsible for inactivating intestinal peptides glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decline in blood glucose levels. The aim of this study was to explore the inhibition activity of small molecule inhibitors to DPP-4 following a computational strategy based on docking studies and molecular dynamics simulations. The thorough docking protocol we applied allowed us to derive good correlation parameters between the predicted binding affinities (pKi) of the DPP-4 inhibitors and the experimental activity values (pIC50). Based on molecular docking receptor-ligand interactions, pharmacophore generation was carried out in order to identify the binding modes of structurally diverse compounds in the receptor active site. Consideration of the permanence and flexibility of DPP-4 inhibitor complexes by means of molecular dynamics (MD) simulation specified that the inhibitors maintained the binding mode observed in the docking study. The present study helps generate new information for further structural optimization and can influence the development of new DPP-4 inhibitors discoveries in the treatment of type-2 diabetes. PMID:27304951

  7. Nuclear arms cleanup

    International Nuclear Information System (INIS)

    The Soviet Union's demise five years ago brought an end to the Cold War, the 45-year arms race between the Soviet superpower and the United States. The euphoria that greeted the end of this bloodless conflict has dampened somewhat, however, as U.S. officials and their counterparts in the former Soviet republics come to grips with its legacy: thousands of highly toxic and politically destabilizing nuclear weapons. With no more perceived need for much of their vast arsenals, the governments have agreed to dismantle large numbers of nuclear warheads. But the agencies involved in this task face a daunting technical and political problem: what to do with the thousands of tons of plutonium and uranium that are the main ingredients of nuclear weapons

  8. Scheduling of Inbound Trucks at a Cross-Docking Facility: Bi-Objective VS Bi-Level Modeling Approaches

    OpenAIRE

    Mihalis M Golias; Saharidis, Georgios K.D.; Maria Boile; Sotirios Theofanis

    2012-01-01

    This paper examines the problem of scheduling of inbound trucks to the inbound doors at a cross-docking facility. The authors optimize for two conflicting objectives: minimize the total service time for all the inbound trucks and minimize the delayed completion of service for a subset of the inbound trucks, which are considered as preferential customers. The problem is formulated as a bi-objective and as a bi-level mixed integer problem. Due to the nature of the former and the complexity of t...

  9. The Asteroid Redirect Mission (ARM): Exploration of a Former Binary NEA?

    Science.gov (United States)

    Abell, P. A.; Mazanek, D. D.; Reeves, D. M.; Chodas, P. W.; Gates, M. M.; Johnson, L. N.; Ticker, R. L.

    2016-01-01

    The National Aeronautics and Space Administration (NASA) is developing the Asteroid Redirect Mission (ARM) as a capability demonstration for future human exploration, including use of high-power solar electric propulsion, which allows for the efficient movement of large masses through deep space. The ARM will also demonstrate the capability to conduct proximity operations with natural space objects and crewed operations beyond the security of quick Earth return. The Asteroid Redirect Robotic Mission (ARRM), currently in formulation, will visit a large near-Earth asteroid (NEA), collect a multi-ton boulder from its surface, conduct a demonstration of a slow push planetary defense technique, and redirect the multi-ton boulder into a stable orbit around the Moon. Once returned to cislunar space in the mid-2020s, astronauts aboard an Orion spacecraft will dock with the robotic vehicle to explore the boulder and return samples to Earth. The ARM is part of NASA's plan to advance technologies, capabilities, and spaceflight experience needed for a human mission to the Martian system in the 2030s. The ARM and subsequent availability of the asteroidal material in cis-lunar space, provide significant opportunities to advance our knowledge of small bodies in the synergistic areas of science, planetary defense, and in-situ resource utilization (ISRU). The current reference target for the ARM is NEA (341843) 2008 EV5, which may have been the primary body of a former binary system (Busch et al., 2011; Tardivel et al., 2016). The ARRM will perform several close proximity operations to investigate the NEA and map its surface. A detailed investigation of this object may allow a better understanding of binary NEA physical characteristics and the possible outcomes for their evolution. An overview of the ARM robotic and crewed segments, including mission operations, and a discussion of potential opportunities for participation with the ARM will be provided in this presentation.

  10. NASA Docking System (NDS) Interface Definitions Document (IDD). Revision F, Dec. 15, 2011

    Science.gov (United States)

    Lewis, James

    2011-01-01

    The NASA Docking System (NDS) mating system supports low approach velocity docking and provides a modular and reconfigurable standard interface, supporting crewed and autonomous vehicles during mating and assembly operations. The NDS is NASA s implementation for the International Docking System Standard (IDSS) using low impact docking technology. All NDS configurations can mate with the configuration specified in the IDSS Interface Definition Document (IDD), Revision A, released May 13, 2011. The NDS evolved from the Low Impact Docking System (LIDS). The term (and its associated acronym), international Low Impact Docking System (iLIDS) is also used to describe this system. NDS and iLIDS may be used interchangeability. Some of the heritage documentation and implementations (e.g., software command names) used on the NDS will continue to use the LIDS acronym.

  11. A High Performance Cloud-Based Protein-Ligand Docking Prediction Algorithm

    OpenAIRE

    Jui-Le Chen; Chun-Wei Tsai; Ming-Chao Chiang; Chu-Sing Yang

    2013-01-01

    The potential of predicting druggability for a particular disease by integrating biological and computer science technologies has witnessed success in recent years. Although the computer science technologies can be used to reduce the costs of the pharmaceutical research, the computation time of the structure-based protein-ligand docking prediction is still unsatisfied until now. Hence, in this paper, a novel docking prediction algorithm, named fast cloud-based protein-ligand docking predictio...

  12. Design and synthesis of new nonsteroidal glucocorticoid modulators through application of an "agreement docking" method.

    Science.gov (United States)

    Barker, Mike; Clackers, Margaret; Demaine, Derek A; Humphreys, Davina; Johnston, Michael J; Jones, Haydn T; Pacquet, Francois; Pritchard, John M; Salter, Mark; Shanahan, Stephen E; Skone, Philip A; Vinader, Victoria M; Uings, Iain; McLay, Iain M; Macdonald, Simon J F

    2005-07-14

    Structurally related glucocorticoid receptor (GR) binders were docked into the GR active site to select the binding mode closest to the true docking mode. This process, termed an "agreement docking method", led to the design of tetrahydronaphthalene 9. The method was validated by the syntheses of 9 and related analogues, which are potent binders of GR. 15a is a partial agonist while 9e and 15a are micromolar antagonists in a mouse mammary tumor virus transactivation assay. PMID:15999989

  13. A study of autonomous docking with an AUV using intelligent controls

    OpenAIRE

    Jantapremjit, Pakpong; Wilson, P.A.; Murphy, Alan J.

    2006-01-01

    Autonomous docking using underwater vehicles will play an important role in long-term underwater explorations and surveys. The autonomous docking mission for an autonomous underwater vehicle at a stationary platform involves a vehicle and a platform matching both position, orientation and velocity. The docking missions therefore require intelligent control systems for precise and soft operations. A study of the sliding mode control and the fuzzy logic controller is pro...

  14. Robot Arms with 3D Vision Capabilities

    OpenAIRE

    Borangiu, Theodor; Alexandru DUMITRACHE

    2010-01-01

    This chapter presented two applications of 3D vision in industrial robotics. The first one allows 3D reconstruction of decorative objects using a laser-based profile scanner mounted on a 6-DOF industrial robot arm, while the scanned part is placed on a rotary table. The second application uses the same profile scanner for 3D robot guidance along a complex path, which is learned automatically using the laser sensor and then followed using a physical tool. While the laser sensor is an expensive...

  15. On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

    DEFF Research Database (Denmark)

    Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

    2011-01-01

    results were compared with a residue-pair potential scoring function (RPScore) and an atomic-detailed scoring function (Zrank). We have combined knowledge-based potentials to score protein-protein poses of decoys of complexes classified either as transient or as permanent protein-protein interactions......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for...... selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

  16. Effective screening strategy using ensembled pharmacophore models combined with cascade docking: application to p53-MDM2 interaction inhibitors.

    Science.gov (United States)

    Xue, Xin; Wei, Jin-Lian; Xu, Li-Li; Xi, Mei-Yang; Xu, Xiao-Li; Liu, Fang; Guo, Xiao-Ke; Wang, Lei; Zhang, Xiao-Jin; Zhang, Ming-Ye; Lu, Meng-Chen; Sun, Hao-Peng; You, Qi-Dong

    2013-10-28

    Protein-protein interactions (PPIs) play a crucial role in cellular function and form the backbone of almost all biochemical processes. In recent years, protein-protein interaction inhibitors (PPIIs) have represented a treasure trove of potential new drug targets. Unfortunately, there are few successful drugs of PPIIs on the market. Structure-based pharmacophore (SBP) combined with docking has been demonstrated as a useful Virtual Screening (VS) strategy in drug development projects. However, the combination of target complexity and poor binding affinity prediction has thwarted the application of this strategy in the discovery of PPIIs. Here we report an effective VS strategy on p53-MDM2 PPI. First, we built a SBP model based on p53-MDM2 complex cocrystal structures. The model was then simplified by using a Receptor-Ligand complex-based pharmacophore model considering the critical binding features between MDM2 and its small molecular inhibitors. Cascade docking was subsequently applied to improve the hit rate. Based on this strategy, we performed VS on NCI and SPECS databases and successfully discovered 6 novel compounds from 15 hits with the best, compound 1 (NSC 5359), K(i) = 180 ± 50 nM. These compounds can serve as lead compounds for further optimization. PMID:24050442

  17. C-arm CT-guided 3D navigation of percutaneous interventions

    International Nuclear Information System (INIS)

    So far C-arm CT images were predominantly used for a precise guidance of an endovascular or intra-arterial therapy. A novel combined 3D-navigation C-arm system now also allows cross-sectional and fluoroscopy controlled interventions. Studies have reported about successful CT-image guided navigation with C-arm systems in vertebroplasty. Insertion of the radiofrequency ablation probe is also conceivable for lung and liver tumors that had been labelled with lipiodol. In the future C-arm CT based navigation systems will probably allow simplified and safer complex interventions and simultaneously reduce radiation exposure. (orig.)

  18. SPACECRAFT DOCKING SIMULATION USING HARDWARE-IN-THE-LOOP SIMULATOR WITH STEWART PLATFORM

    Institute of Scientific and Technical Information of China (English)

    Huang Qitao; Jiang Hongzhou; Zhang Shangying; Han Junwei

    2005-01-01

    A ground-based hardware-in-the-loop (HIL) simulation system with hydraulically driven Stewart platform for spacecraft docking simulation is presented. The system is used for simulating docking process of the on-orbit spacecraft. Principle and structure of the six-degree-of-freedom simulation system are introduced. The docking process dynamic of the vehicles is modeled. Experiment results and mathematical simulation data are compared to validating the simulation system. The comparisons of the results prove that the simulation system proposed can effectively simulate the on-orbit docking process of the spacecraft.

  19. Essential role of Elmo1 in Dock2-dependent lymphocyte migration

    OpenAIRE

    Stevenson, Catherine; de la Rosa, Gonzalo; Anderson, Christopher S.; Murphy, Patrick S.; Capece, Tara; Elliott, Minsoo Kim and Michael R.

    2014-01-01

    Elmo1 and Elmo2 are highly homologous cytoplasmic adapter proteins that interact with Dock family guanine nucleotide exchange factors to promote activation of the small GTPase Rac. In T lymphocytes, Dock2 is essential for CCR7- and CXCR4-dependent Rac activation and chemotaxis, but the role of Elmo proteins in regulating Dock2 function in primary T cells is not known. Here we show that endogenous Elmo1 but not Elmo2 interacts constitutively with Dock2 in mouse and human primary T cells. CD4+ ...

  20. International security and arms control

    International Nuclear Information System (INIS)

    The end of the cold war also ended the focus on the bilateral approach to arms control and disarmament. Key concepts of security needed to be revisited, along with their implications for the disarmament and arms control agenda. Though there is currently a unipolar global security environment, there remain important tasks on the multilateral arms control agenda. The major task is that of reducing and eliminating weapons of mass destruction, especially nuclear weapons. The author contends that maintaining reliance on the nuclear-weapons option makes little sense in a time when the major Powers are strengthening their partnerships in economics, trade, peacemaking and building. (author)

  1. ARM Lead Mentor Selection Process

    Energy Technology Data Exchange (ETDEWEB)

    Sisterson, DL

    2013-03-13

    The ARM Climate Research Facility currently operates more than 300 instrument systems that provide ground-based observations of the atmospheric column. To keep ARM at the forefront of climate observations, the ARM infrastructure depends heavily on instrument scientists and engineers, also known as Instrument Mentors. Instrument Mentors must have an excellent understanding of in situ and remote-sensing instrumentation theory and operation and have comprehensive knowledge of critical scale-dependent atmospheric processes. They also possess the technical and analytical skills to develop new data retrievals that provide innovative approaches for creating research-quality data sets.

  2. Novel Kidins220/ARMS Splice Isoforms: Potential Specific Regulators of Neuronal and Cardiovascular Development.

    Directory of Open Access Journals (Sweden)

    Nathalie Schmieg

    Full Text Available Kidins220/ARMS is a transmembrane protein playing a crucial role in neuronal and cardiovascular development. Kidins220/ARMS is a downstream target of neurotrophin receptors and interacts with several signalling and trafficking factors. Through computational modelling, we found two potential sites for alternative splicing of Kidins220/ARMS. The first is located between exon 24 and exon 29, while the second site replaces exon 32 by a short alternative terminal exon 33. Here we describe the conserved occurrence of several Kidins220/ARMS splice isoforms at RNA and protein levels. Kidins220/ARMS splice isoforms display spatio-temporal regulation during development with distinct patterns in different neuronal populations. Neurotrophin receptor stimulation in cortical and hippocampal neurons and neuroendocrine cells induces specific Kidins220/ARMS splice isoforms and alters the appearance kinetics of the full-length transcript. Remarkably, alternative terminal exon splicing generates Kidins220/ARMS variants with distinct cellular localisation: Kidins220/ARMS containing exon 32 is targeted to the plasma membrane and neurite tips, whereas Kidins220/ARMS without exon 33 mainly clusters the full-length protein in a perinuclear intracellular compartment in PC12 cells and primary neurons, leading to a change in neurotrophin receptor expression. Overall, this study demonstrates the existence of novel Kidins220/ARMS splice isoforms with unique properties, revealing additional complexity in the functional regulation of neurotrophin receptors, and potentially other signalling pathways involved in neuronal and cardiovascular development.

  3. Developing a Comparative Docking Protocol for the Prediction of Peptide Selectivity Profiles: Investigation of Potassium Channel Toxins

    Directory of Open Access Journals (Sweden)

    Serdar Kuyucak

    2012-02-01

    Full Text Available During the development of selective peptides against highly homologous targets, a reliable tool is sought that can predict information on both mechanisms of binding and relative affinities. These tools must first be tested on known profiles before application on novel therapeutic candidates. We therefore present a comparative docking protocol in HADDOCK using critical motifs, and use it to “predict” the various selectivity profiles of several major αKTX scorpion toxin families versus Kv1.1, Kv1.2 and Kv1.3. By correlating results across toxins of similar profiles, a comprehensive set of functional residues can be identified. Reasonable models of channel-toxin interactions can be then drawn that are consistent with known affinity and mutagenesis. Without biological information on the interaction, HADDOCK reproduces mechanisms underlying the universal binding of αKTX-2 toxins, and Kv1.3 selectivity of αKTX-3 toxins. The addition of constraints encouraging the critical lysine insertion confirms these findings, and gives analogous explanations for other families, including models of partial pore-block in αKTX-6. While qualitatively informative, the HADDOCK scoring function is not yet sufficient for accurate affinity-ranking. False minima in low-affinity complexes often resemble true binding in high-affinity complexes, despite steric/conformational penalties apparent from visual inspection. This contamination significantly complicates energetic analysis, although it is usually possible to obtain correct ranking via careful interpretation of binding-well characteristics and elimination of false positives. Aside from adaptations to the broader potassium channel family, we suggest that this strategy of comparative docking can be extended to other channels of interest with known structure, especially in cases where a critical motif exists to improve docking effectiveness.

  4. IDENTIFICATION OF PHARMACOLOGICAL TARGETS COMBINING DOCKING AND MOLECULAR DYNAMICS SIMULATIONS

    Directory of Open Access Journals (Sweden)

    Ilizaliturri-Flores Ian

    2013-01-01

    Full Text Available Studies that include both experimental data and computational simulations (in silico have increased in number because the techniques are complementary. In silico methodologies are currently an essential component of drug design; moreover, identification and optimization of the best ligand based on the structures of biomolecules are common scientific challenges. Geometric structural properties of biomolecules explain their behavior and interactions and when this information is used by a combination of algorithms, a dynamic model based on atomic details can be produced. Docking studies enable researchers to determine the best position for a ligand to bind on a macromolecule, whereas Molecular Dynamics (MD simulations describe the relevant interactions that maintain this binding. MD simulations have the advantage of illustrating the macromolecule movements in more detail. In the case of a protein, the side chain, backbone and domain movements can explain how ligands are trapped during different conformational states. Additionally, MD simulations can depict several binding sites of ligands that can be explored by docking studies, sampling many protein conformations. Following the previously mentioned strategy, it is possible to identify each binding site that might be able to accommodate different ligands through atomic motion. Another important advantage of MD is to explore the movement of side chains of key catalytic residues, which could provide information about the formation of transition states of a protein. All this information can be used to propose ligands and their most probable site of interaction, which are daily tasks of drug design. In this review, the most frequent criteria that are considered when determining pharmacological targets are gathered, particularly when docking and MD are combined.

  5. Ligand pose and orientational sampling in molecular docking.

    Directory of Open Access Journals (Sweden)

    Ryan G Coleman

    Full Text Available Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys-Enhanced (DUD-E benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20,000 molecular orientations in the binding site (and so from about 1×10(10 to 4×10(10 to 1×10(11 to 2×10(11 to 5×10(11 mean atoms scored per target, since multiple conformations are sampled per orientation, the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.

  6. Spacecraft Rendevouz and Docking. An Autonomy assisted Human Operator Approach

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Thuesen, Gøsta

    1999-01-01

    .The method described generates, based on a single camera and a priory information about the target vehicle and orbit data, all necessary guidance information for closed loop autonomous navigation, from first detection at far distance to a close up hold point. Furthermore, the system provides relative pose...... based entirely on direct human supervision and control.This paper describes a vision based system and methodology, that autonomously generates accurate guidance information that may assist a human operator in performing the tasks associated with both the rendezvous and docking navigation procedures...

  7. Laser space rendevous and docking trade-off

    Science.gov (United States)

    1974-01-01

    A spaceborne LADAR sensor, which will meet the requirements for rendezvous and docking with a cooperative object in synchronous orbit is presented. The sensor is being configured around a pulsed CO2 laser which can be constructed and deployed using technology which presently exists or is being developed, and which appears to lend itself very well to the envisioned family of space missions. In order to determine the applicability of the type of sensor being considered, the performance of a family of candidate sensors is being traded off as a function of size, weight, and power consumption. The maximum ranges being considered are 50, 100, 200, and 300 nautical miles.

  8. A strongly goal-directed close-range vision system for spacecraft docking

    Science.gov (United States)

    Boyer, Kim L.; Goddard, Ralph E.

    1991-01-01

    In this presentation, we will propose a strongly goal-oriented stereo vision system to establish proper docking approach motions for automated rendezvous and capture (AR&C). From an input sequence of stereo video image pairs, the system produces a current best estimate of: contact position; contact vector; contact velocity; and contact orientation. The processing demands imposed by this particular problem and its environment dictate a special case solution; such a system should necessarily be, in some sense, minimalist. By this we mean the system should construct a scene description just sufficiently rich to solve the problem at hand and should do no more processing than is absolutely necessary. In addition, the imaging resolution should be just sufficient. Extracting additional information and constructing higher level scene representations wastes energy and computational resources and injects an unnecessary degree of complexity, increasing the likelihood of malfunction. We therefore take a departure from most prior stereopsis work, including our own, and propose a system based on associative memory. The purpose of the memory is to immediately associate a set of motor commands with a set of input visual patterns in the two cameras. That is, rather than explicitly computing point correspondences and object positions in world coordinates and trying to reason forward from this information to a plan of action, we are trying to capture the essence of reflex behavior through the action of associative memory. The explicit construction of point correspondences and 3D scene descriptions, followed by online velocity and point of impact calculations, is prohibitively expensive from a computational point of view for the problem at hand. Learned patterns on the four image planes, left and right at two discrete but closely spaced instants in time, will be bused directly to infer the spacecraft reaction. This will be a continuing online process as the docking collar approaches.

  9. UNC-31/CAPS docks and primes dense core vesicles in C. elegans neurons.

    Science.gov (United States)

    Lin, Xian-Guang; Ming, Min; Chen, Mao-Rong; Niu, Wei-Pin; Zhang, Yong-Deng; Liu, Bei; Jiu, Ya-Ming; Yu, Jun-Wei; Xu, Tao; Wu, Zheng-Xing

    2010-07-01

    UNC-31 or its mammalian homologue, Ca(2+)-dependent activator protein for secretion (CAPS), is indispensable for exocytosis of dense core vesicle (DCV) and synaptic vesicle (SV). From N- to the C-terminus, UNC-31 contains putative functional domains, including dynactin 1 binding domain (DBD), C2, PH, (M)UNC-13 homology domain (MHD) and DCV binding domain (DCVBD), the last four we examined in this study. We employed UNC-31 null mutant C. elegans worms to examine whether UNC-31 functions could be rescued by ectopic expression of full length UNC-31 vs each of these four domain-deleted mutants. Full length UNC-31 cDNA rescued the phenotypes of C. elegans null mutants in response to Ca(2+)-elevation in ALA neurons. Surprisingly, MHD deletion also rescued UNC-31 exocytotic function in part because the relatively high Ca(2+) level (pre-flash Ca(2+) was 450 nM) used in the capacitance study could bypass the MHD defect. Nonetheless, the three other domain-truncation cDNAs had almost no rescue on Ca(2+) evoked secretion. Importantly, this genetic null mutant rescue strategy enabled physiological studies at levels of whole organism to single cells, such as locomotion assay, pharmacological study of neurotransmission at neuromuscular junction, in vivo neuropeptide release measurement and analysis of vesicular docking. Our results suggest that each of these UNC-31 domains support distinct sequential molecular actions of UNC-31 in vesicular exocytosis, including steps in vesicle tethering and docking that bridge vesicle with plasma membrane, and subsequently priming vesicle by initiating the formation of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) core complex. PMID:20515653

  10. Binding between Saikosaponin C and Human Serum Albumin by Fluorescence Spectroscopy and Molecular Docking

    Directory of Open Access Journals (Sweden)

    Yi-Cun Chen

    2016-01-01

    Full Text Available Saikosaponin C (SSC is one of the major active constituents of dried Radix bupleuri root (Chaihu in Chinese that has been widely used in China to treat a variety of conditions, such as liver disease, for many centuries. The binding of SSC to human serum albumin (HSA was explored by fluorescence, circular dichroism (CD, UV-vis spectrophotometry, and molecular docking to understand both the pharmacology and the basis of the clinical use of SSC/Chaihu. SSC produced a concentration-dependent quenching effect on the intrinsic fluorescence of HSA, accompanied by a blue shift in the fluorescence spectra. The Stern-Volmer equation showed that this quenching was dominated by static quenching. The binding constant of SSC with HSA was 3.72 × 103 and 2.99 × 103 L·mol−1 at 26 °C and 36 °C, respectively, with a single binding site on each SSC and HSA molecule. Site competitive experiments demonstrated that SSC bound to site I (subdomain IIA and site II (subdomain IIIA in HSA. Analysis of thermodynamic parameters indicated that hydrogen bonding and van der Waals forces were mostly responsible for SSC-HSA association. The energy transfer efficiency and binding distance between SSC and HSA was calculated to be 0.23 J and 2.61 nm at 26 °C, respectively. Synchronous fluorescence and CD measurements indicated that SSC affected HSA conformation in the SSC-HSA complex. Molecular docking supported the experimental findings in conformational changes, binding sites and binding forces, and revealed binding of SSC at the interface between subdomains IIA-IIB.

  11. Arms control: misplaced focus

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, W.A.; Derber, C.

    1986-03-01

    Most of the nuclear debate consists of arguments about which weapons systems should be built, controlled, canceled, frozen, or retired. Short of virtually complete, multilateral nuclear disarmament, however, no change in the pace, balance, or even the direction of the arms race can make much difference in the risk of nuclear war, the damage should one occur, or the division of international political power. This includes Star Wars, the nuclear freeze, and even large cuts in or stabilization of offensive nuclear arsenals. A better starting point for nuclear politics would be the insight that nuclear weapons have completely changed the logic of power as it has been handed down through the ages. Military force, perfected to its highest level, has invalidated itself - for in a nuclearized world, any resort to force by a nuclear power risks escalation to its ultimate level, and thus to oblivion for all. Trying to rationalize and control the ultimate force is far less realistic and important than limiting the provocation of conflict and the use of force at lower, non-nuclear levels - by the United States, it clients, and, to the extent possible, its adversaries. 13 references.

  12. ARM Standards Policy Committee Report

    Energy Technology Data Exchange (ETDEWEB)

    Cialella, A; Jensen, M; Koontz, A; McFarlane, S; McCoy, R; Monroe, J; Palanisamy, G; Perez, R; Sivaraman, C

    2012-09-19

    Data and metadata standards promote the consistent recording of information and are necessary to ensure the stability and high quality of Atmospheric Radiation Measurement (ARM) Climate Research Facility data products for scientific users. Standards also enable automated routines to be developed to examine data, which leads to more efficient operations and assessment of data quality. Although ARM Infrastructure agrees on the utility of data and metadata standards, there is significant confusion over the existing standards and the process for allowing the release of new data products with exceptions to the standards. The ARM Standards Policy Committee was initiated in March 2012 to develop a set of policies and best practices for ARM data and metadata standards.

  13. Torque-Wrench Extension Arm

    Science.gov (United States)

    Pacala, T. J.; Trujillo, D. D.; Laudenslager, J. B.

    1984-01-01

    Torque-wrench extension arm makes possible to apply torque to bolt, screw, or nut inaccessible to conventional wrenches or in areas where wrench cannot be manipulated. Used in narrow pockets and behind panels and walls.

  14. 21 CFR 890.3640 - Arm sling.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Arm sling. 890.3640 Section 890.3640 Food and... PHYSICAL MEDICINE DEVICES Physical Medicine Prosthetic Devices § 890.3640 Arm sling. (a) Identification. An arm sling is a device intended for medical purposes to immobilize the arm, by means of a fabric...

  15. 49 CFR 234.223 - Gate arm.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Gate arm. 234.223 Section 234.223 Transportation... Maintenance Standards § 234.223 Gate arm. Each gate arm, when in the downward position, shall extend across... clearly viewed by approaching highway users. Each gate arm shall start its downward motion not less...

  16. Two giant stellar complexes

    Science.gov (United States)

    Efremov, Yu. N.; Efremov, E. Yu.

    Common star complexes are huge (0.3-1 kpc in diameter) groups of relatively young stars, associations and clusters. The complexes usually form regular chains along spiral arms of grand design galaxies, being evidently formed and supported by magneto- gravitational instability developing along an arm. Special attention is given to a few large complexes which have signatures of gravitational boundness, such as round shape and high central density. Concentrations of stars and clusters in such a complex in M51 galaxy were found in this paper; we concluded it is possible to suggest that the complex is gravitationally bound. It is also stressed that some properties of the giant complex in NGC 6946 (such as its semicircular and sharp Western edge) are still enigmatic.

  17. Combinatorial Multi-Armed Bandit and Its Extension to Probabilistically Triggered Arms

    OpenAIRE

    Chen, Wei; Wang, Yajun; Yuan, Yang; Wang, Qinshi

    2014-01-01

    We define a general framework for a large class of combinatorial multi-armed bandit (CMAB) problems, where subsets of base arms with unknown distributions form super arms. In each round, a super arm is played and the base arms contained in the super arm are played and their outcomes are observed. We further consider the extension in which more based arms could be probabilistically triggered based on the outcomes of already triggered arms. The reward of the super arm depends on the outcomes of...

  18. Waste Isolation Pilot Plant TruDock crane system analysis

    International Nuclear Information System (INIS)

    The WIPP TruDock crane system located in the Waste Handling Building was identified in the WIPP Safety Analysis Report (SAR), November 1995, as a potential accident concern due to failures which could result in a dropped load. The objective of this analysis is to evaluate the frequency of failure of the TruDock crane system resulting in a dropped load and subsequent loss of primary containment, i.e. drum failure. The frequency of dropped loads was estimated to be 9.81E-03/year or approximately one every 102 years (or, for the 25% contingency, 7.36E-03/year or approximately one every 136 years). The dominant accident contributor was the failure of the cable/hook assemblies, based on failure data obtained from NUREG-0612, as analyzed by PLG, Inc. The WIPP crane system undergoes a rigorous test and maintenance program, crane operation is discontinued following any abnormality, and the crane operator and load spotter are required to be trained in safe crane operation, therefore it is felt that the WIPP crane performance will exceed the data presented in NUREG-0612 and the estimated failure frequency is felt to be conservative

  19. Attitudes of Dutch Pig Farmers Towards Tail Biting and Tail Docking

    NARCIS (Netherlands)

    Bracke, M.B.M.; Lauwere, de C.C.; Wind, S.M.M.; Zonderland, J.J.

    2013-01-01

    The Dutch policy objective of a fully sustainable livestock sector without mutilations by 2023 is not compatible with the routine practice of tail docking to minimize the risk of tail biting. To examine farmer attitudes towards docking, a telephone survey was conducted among 487 conventional and 33

  20. 48 CFR 52.247-40 - Ex Dock, Pier, or Warehouse, Port of Importation.

    Science.gov (United States)

    2010-10-01

    ... Warehouse, Port of Importation. 52.247-40 Section 52.247-40 Federal Acquisition Regulations System FEDERAL... Provisions and Clauses 52.247-40 Ex Dock, Pier, or Warehouse, Port of Importation. As prescribed in 47.303-12..., pier, or warehouse, port of importation: Ex Dock, Pier, or Warehouse, Port of Importation (APR 1984)...

  1. Satellite-rocket docking ring recognition method based on mathematical morphology

    Science.gov (United States)

    Xu, Zhiqiang; Shang, Yang; Ma, Xuan

    2015-10-01

    Satellite-rocket docking ring recognition method based on mathematical morphology is presented in this paper, according to the geometric and grayscale characteristics of the docking ring typical structure. The docking ring used in this paper is a circle with a cross in the middle. Most of spacecrafts are transported into orbit by rocket, and they retain the connection component with the rocket. The tracing spacecraft should capture the target spacecraft first before operating the target spacecraft. The docking ring is one of the typical parts of a spacecraft, and it can be recognized automatically. Thereby we can capture the spacecraft through the information of the docking ring. Firstly a multi-step mathematical morphology processing is applied to the image of the target spacecraft with different structure element, followed by edge detection and line detection, and finally docking ring typical structure is located in the image by relative geometry analysis. The images used in this paper are taken of real satellite in lab. The docking ring can be recognized when the distance between the two spacecraft is different. The results of physical simulation experiment show that the method in this paper can recognize docking ring typical structure accurately when the tracing spacecraft is approaching the target spacecraft.

  2. DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations

    Directory of Open Access Journals (Sweden)

    Alberto Cuzzolin

    2015-05-01

    Full Text Available Virtual screening (VS is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS exploits knowledge about the three-dimensional (3D structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users’ proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1 are discussed as validation test.

  3. Developing a cross-docking network design model under uncertain environment

    Science.gov (United States)

    Seyedhoseini, S. M.; Rashid, Reza; Teimoury, E.

    2014-09-01

    Cross-docking is a logistic concept, which plays an important role in supply chain management by decreasing inventory holding, order packing, transportation costs and delivery time. Paying attention to these concerns, and importance of the congestion in cross docks, we present a mixed-integer model to optimize the location and design of cross docks at the same time to minimize the total transportation and operating costs. The model combines queuing theory for design aspects, for that matter, we consider a network of cross docks and customers where two M/M/c queues have been represented to describe operations of indoor trucks and outdoor trucks in each cross dock. To prepare a perfect illustration for performance of the model, a real case also has been examined that indicated effectiveness of the proposed model.

  4. Two-dimensional PSD based automatic docking of self-reconfiguration modular exploration robot system

    Institute of Scientific and Technical Information of China (English)

    Zhang Liping; Ma Shugen; Li Bin; Zhang Zheng; Cao Binggang

    2007-01-01

    Based on the design of a docking mechanism, this paper thoroughly investigates the space automatic docking of self-reconfiguration modular exploration robot system (RMERS). The method that leads robot to achieve space docking by using two-dimensional PSD is put forward innovatively for the median size robot system. At the same time, in order to enlarge the detecting extension and the precision of PSD and reduce its dependence on lighting signal, the PSD was remade by increasing the optical device over its light-sensitive surface. The emission board and LED light scheduling were designed according to docking arithmetic, and the operating principle of docking process was analyzed based on these. The simulation experiments were carried out and their results are presented.

  5. Accessible high-throughput virtual screening molecular docking software for students and educators.

    Directory of Open Access Journals (Sweden)

    Reed B Jacob

    2012-05-01

    Full Text Available We survey low cost high-throughput virtual screening (HTVS computer programs for instructors who wish to demonstrate molecular docking in their courses. Since HTVS programs are a useful adjunct to the time consuming and expensive wet bench experiments necessary to discover new drug therapies, the topic of molecular docking is core to the instruction of biochemistry and molecular biology. The availability of HTVS programs coupled with decreasing costs and advances in computer hardware have made computational approaches to drug discovery possible at institutional and non-profit budgets. This paper focuses on HTVS programs with graphical user interfaces (GUIs that use either DOCK or AutoDock for the prediction of DockoMatic, PyRx, DockingServer, and MOLA since their utility has been proven by the research community, they are free or affordable, and the programs operate on a range of computer platforms.

  6. Scheduling Trucks in Multi-Door Cross Docking Systems: An Adaptive Genetic Algorithm with a Dispatching Rule

    OpenAIRE

    Byung Soo Kim; Cheol Min Joo

    2015-01-01

    One of the most important operational management problems of a cross docking system is the truck scheduling problem. Cross docking is a logistics management concept in which products delivered to a distribution center by inbound trucks are immediately sorted out, routed and loaded into outbound trucks for delivery to customers. The truck scheduling problem in a multi-door cross docking system considered in this paper comprises the assignment of trucks to dock doors and the determination of do...

  7. Empty arms : the effect of the arms trade on mothers and children

    OpenAIRE

    Southall, DP; O'Hare, BAM

    2002-01-01

    Trading in arms, both legal and illegal, is highly detrimental to the health of mothers and children in the countries where armed conflict occurs. But do the powerful arms trading countries want to address the problems they are causing?.

  8. Docking of anti-HIV-1 oxoquinoline-acylhydrazone derivatives as potential HSV-1 DNA polymerase inhibitors

    Science.gov (United States)

    Yoneda, Julliane Diniz; Albuquerque, Magaly Girão; Leal, Kátia Zaccur; Santos, Fernanda da Costa; Batalha, Pedro Netto; Brozeguini, Leonardo; Seidl, Peter R.; de Alencastro, Ricardo Bicca; Cunha, Anna Cláudia; de Souza, Maria Cecília B. V.; Ferreira, Vitor F.; Giongo, Viveca A.; Cirne-Santos, Cláudio; Paixão, Izabel C. P.

    2014-09-01

    Although there are many antiviral drugs available for the treatment of herpes simplex virus (HSV) infections, still the synthesis of new anti-HSV candidates is an important strategy to be pursued, due to the emergency of resistant HSV strains mainly in human immunodeficiency virus (HIV) co-infected patients. Some 1,4-dihydro-4-oxoquinolines, such as PNU-183792 (1), show a broad spectrum antiviral activity against human herpes viruses, inhibiting the viral DNA polymerase (POL) without affecting the human POLs. Thus, on an ongoing antiviral research project, our group has synthesized ribonucleosides containing the 1,4-dihydro-4-oxoquinoline (quinolone) heterocyclic moiety, such as the 6-Cl derivative (2), which is a dual antiviral agent (HSV-1 and HIV-1). Molecular dynamics simulations of the complexes of 1 and 2 with the HSV-1 POL suggest that structural modifications of 2 should increase its experimental anti-HSV-1 activity, since its ribosyl and carboxyl groups are highly hydrophilic to interact with a hydrophobic pocket of this enzyme. Therefore, in this work, comparative molecular docking simulations of 1 and three new synthesized oxoquinoline-acylhydrazone HIV-1 inhibitors (3-5), which do not contain those hydrophilic groups, were carried out, in order to access these modifications in the proposition of new potential anti-HSV-1 agents, but maintaining the anti-HIV-1 activity. Among the docked compounds, the oxoquinoline-acylhydrazone 3 is the best candidate for an anti-HSV-1 agent, and, in addition, it showed anti-HIV-1 activity (EC50 = 3.4 ± 0.3 μM). Compounds 2 and 3 were used as templates in the design of four new oxoquinoline-acylhydrazones (6-9) as potential anti-HSV-1 agents to increase the antiviral activity of 2. Among the docked compounds, oxoquinoline-acylhydrazone 7 was selected as the best candidate for further development of dual anti-HIV/HSV activity.

  9. BioShaDock: a community driven bioinformatics shared Docker-based tools registry [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    François Moreews

    2015-12-01

    Full Text Available Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

  10. ANALISA TEKNIS DAN EKONOMIS SISTEM PERBAIKAN DAUN PROPELLER YANG PATAH PADA KM. MANDIRI DUA TANPA DOCKING

    Directory of Open Access Journals (Sweden)

    Parlindungan Manik

    2012-03-01

    Full Text Available At a sailing in a territorial to sea or river, ship propeller frequently collide object or foreign object which float, causing damage at propeller, throw in the form of curving, crack or broken at propeller blade. When this damage do not improve immediately; repaired will generate harm effect to ship construction or parts of machinery. Therefore ship should be immediately to repair (emergency docking to improve the propeller. But is not easy to get docking space to repair because docking space schedule is very strike, existing graving dock in country. So that ship have to kick one's heels to be able to docking space, which meaning of big loss of time and also expense. The air of this research technical analysis possibility implementation to propeller repairf by floating repair system in territorial water closest with damage location of propeller and compare efficiency economic value and time if repair of propeller done in graving dock or executed by floating repair in graving dock. In this research, repair propeller without docking can be executed by arranging ship trim by arranging ballast tank to be reached space which last for working. Hereinafter worked repair of blade propeller thickly , pitch, aerofoil, wide of blade, obtained mains material type from source which have been collected by either from Owner Surveyor, picture - technique picture and also blade propeller which still goodness. Result of analysis indicate that technically repair of propeller which broken can be executed without docking and economically will be more be efficient up to 700%,in comparison with executed in Graving Dock, and will be more be efficient up to 300% when compared with executed in floating repair system

  11. Design of Robotic Arm Control System Mimics Human Arm Motion

    Directory of Open Access Journals (Sweden)

    A. Salam Al-Ammri

    2013-01-01

    Full Text Available This paper presents a control system to make the robotic hand mimic human hand motion in real time and offline mode. The human hand tracking system is a wearable sensing arm (potentiometers used to determine the position in space and to sense the grasping task of human hand. The maskable sensing arm was designed with same geometrical arrangement of robotic hand that needs to be controlled. The control software of a robot was implemented using Visual Basic and supported with graphical user interface (GUI. The control algorithm depends on joint to joint mapping method to match between the motions at each joint of portable sensing arm with corresponding joint of a robot in order to make the robot mimic the motion.

  12. Application repository and science gateway for running molecular docking and dynamics simulations.

    Science.gov (United States)

    Terstyanszky, Gabor; Kiss, Tamas; Kukla, Tamas; Lichtenberger, Zsolt; Winter, Stephen; Greenwell, Pamela; McEldowney, Sharron; Heindl, Hans

    2012-01-01

    Molecular docking and dynamics studies are of considerable importance in a range of disciplines including molecular biology, drug design, environmental studies, psychology, etc. Using in silico tools to support or even to substitute wet laboratory work could help better focusing the laboratory experiments resulting not only in considerable saving of resources but also increasing the number of molecules and scenarios investigated. There are several software packages that support in silico modeling. However, these tools require lot of compute resources and special technical knowledge. As a result, many bio-scientists cannot use them. The paper describes a science gateway based solution which provides access to Distributed Computing Infrastructures such as clouds, desktop and service grids. This environment enables bio-scientists to execute simple molecular modeling scenarios or build more complex use-cases from existing building blocks while hiding the technical details of the infrastructure. Four scenarios have been defined and deconstructed in order to identify common building blocks supporting a large number of complex use-cases. A reference implementation for the first scenario regarding the impact on indicator species of pharmaceuticals released into water courses has been implemented on the EDGI infrastructure, demonstrating the feasibility of the approach. PMID:22942006

  13. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

    Science.gov (United States)

    Ohno, Kazuki; Mitsui, Takashi; Tanida, Yoshiaki; Matsuura, Azuma; Fujitani, Hideaki; Niimi, Tatsuya; Orita, Masaya

    2011-02-01

    Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein/ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1)/inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects. PMID:20480380

  14. Design and Development of Ball Catching Robotic Arm

    Directory of Open Access Journals (Sweden)

    Kartik Sharma

    2012-08-01

    Full Text Available This paper presents a ball catching robotic arm system with 3DOF assembled from the commercially available parts. Other than the previous research work a mechatronically complex system were designed. We have designed a very simple arm which is able to move for catching the ball when it has to move. The given robotic arm system is low cost implementation compare to the previous one. In this system, a single camera system is use to perceive the trajectory of the ball, the system detects the ball in each frame with the help of a fast mean shift algorithm. It calculates the shift of the mean of the identified color intensity and according to that it sends the control commands over the serial port to the robotic arm via ZigBee. The basic objective to catch the flying object at the expected location. This catcher robotic arm can catch the ball thrown to it from 5-6 meter with an average success rate of 70-75%.

  15. NASA's Asteroid Redirect Mission (ARM)

    Science.gov (United States)

    Abell, Paul; Mazanek, Dan; Reeves, David; Naasz, Bo; Cichy, Benjamin

    2015-11-01

    The National Aeronautics and Space Administration (NASA) is developing a robotic mission to visit a large near-Earth asteroid (NEA), collect a multi-ton boulder from its surface, and redirect it into a stable orbit around the Moon. Once returned to cislunar space in the mid-2020s, astronauts will explore the boulder and return to Earth with samples. This Asteroid Redirect Mission (ARM) is part of NASA’s plan to advance the technologies, capabilities, and spaceflight experience needed for a human mission to the Martian system in the 2030s. Subsequent human and robotic missions to the asteroidal material would also be facilitated by its return to cislunar space. Although ARM is primarily a capability demonstration mission (i.e., technologies and associated operations), there exist significant opportunities to advance our knowledge of small bodies in the synergistic areas of science, planetary defense, asteroidal resources and in-situ resource utilization (ISRU), and capability and technology demonstrations. In order to maximize the knowledge return from the mission, NASA is organizing an ARM Investigation Team, which is being preceded by the Formulation Assessment and Support Team. These teams will be comprised of scientists, technologists, and other qualified and interested individuals to help plan the implementation and execution of ARM. An overview of robotic and crewed segments of ARM, including the mission requirements, NEA targets, and mission operations, will be provided along with a discussion of the potential opportunities associated with the mission.

  16. Dinuclear Cu(II) complexes of compartmental Schiff base ligands formed from unsymmetrical tripodal amines of varying arm lengths: Crystal structure of [Cu2L1](ClO4)2 and theoretical studies

    Science.gov (United States)

    Keypour, Hassan; Shayesteh, Maryam; Rezaeivala, Majid; Sayin, Koray

    2016-05-01

    Three new dinuclear copper complexes were synthesized via condensation reaction of three new unsymmetrical N-capped tripodal amines and 2,6-diformyl-4-methylphenol, in the presence of copper(II) perchlorate. The solid-state structure of the dinuclear complex, [Cu2L1](ClO4)2, has been determined by X-ray crystallography, showing that the CuII centers have distorted square-pyramidal geometry with N3O2 coordination. The copper (II) ions are bridged by phenolic and hydroxyalkyl groups when in both cases, deprotonation of the hydrogen atoms of the OH groups occurs. The distance between the copper atoms is 3.062 Å. This compound consists of the dication [Cu2L1]2+ and two ClO4- anions in which one of ClO4- groups has a week interaction with one of the Cu atoms. All complexes were characterized by a variety of physico-chemical techniques such as elemental analyses, IR, mass spectra, conductivity measurements and electronic spectral studies. Computational investigation of mentioned binuclear Cu(II) complexes was done by using M062X method with LANL2DZ basis set in vacuo.

  17. Radiolabeling, biological evaluation and molecular docking of delafloxacin. A novel methicillin-resistant Staphylococcus aureus infection radiotracer

    International Nuclear Information System (INIS)

    Labeling of delafloxacin with technetium-99m (99mTc) and its characterization in terms of in vitro stability and in vitro binding with methicillin-resistant Staphylococcus aureus (MRSA) were explored. Optimum amounts of reactants were 2.5 mg delafloxacin, 125 µg stannous chloride dihydrate and ∼125 MBq pertechnetate. The 99mTc-delafloxacin was stable up to 6 h. Molecular modeling and docking studies showed that the complex will stabilize the DNA-topoisomerase IIA cleavage complex and inhibit strands separation. The in vivo evaluation showed highest specific accumulation in the live MRSA model (8 %) compared to other models. All gathered data supported the usefulness of 99mTc-delafloxacin as a MRSA radiotracer. (author)

  18. A comparison of heuristic search algorithms for molecular docking.

    Science.gov (United States)

    Westhead, D R; Clark, D E; Murray, C W

    1997-05-01

    This paper describes the implementation and comparison of four heuristic search algorithms (genetic algorithm, evolutionary programming, simulated annealing and tabu search) and a random search procedure for flexible molecular docking. To our knowledge, this is the first application of the tabu search algorithm in this area. The algorithms are compared using a recently described fast molecular recognition potential function and a diverse set of five protein-ligand systems. Statistical analysis of the results indicates that overall the genetic algorithm performs best in terms of the median energy of the solutions located. However, tabu search shows a better performance in terms of locating solutions close to the crystallographic ligand conformation. These results suggest that a hybrid search algorithm may give superior results to any of the algorithms alone. PMID:9263849

  19. Robot Docking Based on Omnidirectional Vision and Reinforcement Learning

    Science.gov (United States)

    Muse, David; Weber, Cornelius; Wermter, Stefan

    We present a system for visual robotic docking using an omnidirectional camera coupled with the actor critic reinforcement learning algorithm. The system enables a PeopleBot robot to locate and approach a table so that it can pick an object from it using the pan-tilt camera mounted on the robot. We use a staged approach to solve this problem as there are distinct sub tasks and different sensors used. Starting with random wandering of the robot until the table is located via a landmark, and then a network trained via reinforcement allows the robot to rum to and approach the table. Once at the table the robot is to pick the object from it. We argue that our approach has a lot of potential allowing the learning of robot control for navigation removing the need for internal maps of the environment. This is achieved by allowing the robot to learn couplings between motor actions and the position of a landmark.

  20. Synthesis, Evaluation and Docking studies of Cholecalciferol Derivative

    Directory of Open Access Journals (Sweden)

    Sultanat

    2014-09-01

    Full Text Available Improved synthesis of 3b-acetoxy-9, 10-seco-19, 8(8-spiro-5(10, 6-cholestadiene has been reported after reacting cholecalciferol acetate with dimethylbutadiene by incorporating BF3·OEt2, SnCl4, ZnBr2, p-TsOH in toluene under Diels-Alder condition to get better yields. Agarose gel electrophoresis showed the potential in vitro DNA damaging nature while as the comet assay depicted the genotoxic nature by mobilizing the tail of the comet in lymphocytes. The molecular docking depicted the intercalation of steroid derivative with minor groove of the DNA molecule and in this configuration the phosphodiester bond of DNA stabilizes the acetoxy group. The bioactivity score and PASS software analysis confirmed the potential physicochemical features of the compound to act as active drug.

  1. Planification des opérations de cross-docking

    OpenAIRE

    Ladier, Anne-Laure; Alpan, Gülgün

    2014-01-01

    Les plateformes de cross-docking permettent d'accélérer les flux logistiques : les produits y sont déchargés, triés et rechargés dans les camions sans stockage intermédiaire. Nous nous intéressons à un problème de planification des opérations dans une telle plateforme, en supposant que les transporteurs communiquent à l'avance leurs créneaux de présence préférés. Outre la modélisation du problème par un programme linéaire, nous proposons deux heuristiques qui décomposent le problème et permet...

  2. SYNTHESIS, DOCKING STUDIES AND ANTIOXIDANT ACTIVITY OF TETRAPEPTIDE FGVY

    Directory of Open Access Journals (Sweden)

    Md. Abdulla

    2011-03-01

    Full Text Available A rational designing of linear Tetrapeptide FGVY was done and was synthesized by solution phase peptide synthesis. The docking studies of designed linear tetrapeptide FGVY was carried out by using Schrodinger Software Solutions, USA. Qikprop results show the ligand FGVY mostly act as antihypertensive and anti coagulant properties. The solution phase synthesis of FGVY is carried out by using Dicyclohexyl carbodiimide (DCC as coupling agents and triethyl amine as base. Structure of synthesized FGVY was confirmed by FTIR, 1H NMR and Mass spectral data, and evaluated for antioxidant property by using 1,1-diphenyl-2-picryl-hydrazil (DPPH. method and the synthesized peptides FGVY possess moderate antioxidant activity.

  3. FACILE SYNTHESIS, DOCKING STUDIES AND ANTIOXIDANT ACTIVITY OF FGVR

    Directory of Open Access Journals (Sweden)

    Himaja M

    2011-08-01

    Full Text Available A rational designing of linear Tetrapeptide FGVR was done and was synthesized by solution phase peptide synthesis. The docking studies of designed linear tetrapeptide FGVR was carried out by using Schrodinger Software Solutions, USA. Qikprop results show the ligand FGVR mostly act as antihypertensive and anti coagulant properties. The solution phase synthesis of FGVR is carried out by using 1-Ethyl-3-(3-dimethylaminopropyl carbodiimide (EDC as coupling agents and N-Methyl morpholine (NMM as base. Structure of synthesized FGVR was confirmed by FTIR, 1H NMR and Mass spectral data, and evaluated for antioxidant property by using 1,1-diphenyl-2-picryl-hydrazil (DPPH. method and the synthesized peptides FGVR possess moderate antioxidant activity.

  4. Scanning ARM Cloud Radar Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Widener, K; Bharadwaj, N; Johnson, K

    2012-06-18

    The scanning ARM cloud radar (SACR) is a polarimetric Doppler radar consisting of three different radar designs based on operating frequency. These are designated as follows: (1) X-band SACR (X-SACR); (2) Ka-band SACR (Ka-SACR); and (3) W-band SACR (W-SACR). There are two SACRs on a single pedestal at each site where SACRs are deployed. The selection of the operating frequencies at each deployed site is predominantly determined by atmospheric attenuation at the site. Because RF attenuation increases with atmospheric water vapor content, ARM's Tropical Western Pacific (TWP) sites use the X-/Ka-band frequency pair. The Southern Great Plains (SGP) and North Slope of Alaska (NSA) sites field the Ka-/W-band frequency pair. One ARM Mobile Facility (AMF1) has a Ka/W-SACR and the other (AMF2) has a X/Ka-SACR.

  5. Nuclear arms: ethics, strategy, politics

    Energy Technology Data Exchange (ETDEWEB)

    Woolsey, R.J. (ed.)

    1984-01-01

    The range of debate over strategy and arms control today is broader than it was in the late 1950s and early 1960s. In part this is because the early 1980s debate has involved questioning of the fundamental notion of deterrence - by no less than the American Catholic bishops. Today's debate has also seen a national nuclear freeze campaign that, although its congressional supporters have held firmly to a bilateral approach, was tilted perceptibly towards unilateralism by noncongressional leaders at their national conference in February 1983. In one way or another the authors wrestle with different aspects of one central question: could the beginning steps for any consensus be possible, in today's climate, on strategic issues. Ethical issues are addressed in the first 3 papers: Charles Krauthammer, On Nuclear Morality; Patrick Glynn, The Moral Case for the Arms Buildup; and Michael Quinlarc, Thinking Deterrence Through. Three chapters on strategic considerations include: Brent Snowcroft, Understanding the US Strategic Arsenal; William J. Perry, Technological Prospects for US Strategic Forces; and Richard Burt, The Strategic and Political Lessons of INF. Arms control and politics is treated in chapters by: Walter B. Slocombe, Arms Control: Prospects; and Colin S. Gray, Arms Control: Problems. The nonnuclear dimensions of strategy are discussed in chapters by Amory B. and L. Hunter Lovins, Reducing Vulnerability - The Energy Jugular; and Robert Kupperman, Vulnerable America. The chapters on space and defense are: Hans Mark, Arms Control and Space Technology; and Newt Gingrich and John Madison, Space and National Defense. The concluding chapters are by Sen. Sam Nunn, The Need to Reshape Military Stategy; and the editor, R. James Woolsey, The Politics of Vulnerability, 1980-1983.

  6. Arm insulation and swimming in cold water.

    Science.gov (United States)

    Lounsbury, David S; Ducharme, Michel B

    2008-09-01

    To test whether adding insulation to the arms would improve cold water swimming performance by delaying swimming failure (SF). Novice (n = 7) and expert (n = 8) swimmers, clothed and equipped with a personal flotation device, each performed two trials in a swimming flume filled with 10 degrees C water. During free swimming (FS), subjects performed swimming until failure, followed by the Heat Escape Lessening Posture. In free swimming with additional insulation (FSA), subjects wore custom-fitted armbands. Trials ended when rectal temperature decreased to 34 degrees C or after 2 h of immersion. Measurements included: rectal and skin temperatures, heat flow, and various appraisals of swimming performance. FSA was thermally advantageous versus FS. Rectal temperature cooling rates during swimming (dT/dt Swim) were faster for FS compared to FSA (0.050 +/- 0.007 degrees C min(-1) vs. 0.042 +/- 0.006 degrees C min(-1), P skin temperature about 10 degrees C warmer, for approximately 70 min (P stroke rate (6.6 str min(-1)) and decreases in stroke length (0.24 m str(-1)) observed. In this simulation of cold water swimming survival, equipping subjects with neoprene armbands appears to have partially preserved muscle function, but with unimpressive effects on overall performance. SF is a complex entity, but is evidently related to both triceps skinfold and arm girth. PMID:18309510

  7. NASA Docking System (NDS) Interface Definitions Document (IDD). Revision C, Nov. 2010

    Science.gov (United States)

    2010-01-01

    The NASA Docking System (NDS) mating system supports low approach velocity docking and provides a modular and reconfigurable standard interface, supporting crewed and autonomous vehicles during mating and assembly operations. The NDS is NASA's implementation for the emerging International Docking System Standard (IDSS) using low impact docking technology. All NDS configurations can mate with the configuration specified in the IDSS Interface Definition Document (IDD) released September 21, 2010. The NDS evolved from the Low Impact Docking System (LIDS). The acronym international Low Impact Docking System (iLIDS) is also used to describe this system. NDS and iLIDS may be used interchangeability. Some of the heritage documentation and implementations (e.g., software command names) used on NDS will continue to use the LIDS acronym. The NDS IDD defines the interface characteristics and performance capability of the NDS, including uses ranging from crewed to autonomous space vehicles and from low earth orbit to deep space exploration. The responsibility for developing space vehicles and for making them technically and operationally compatible with the NDS rests with the vehicle providers. Host vehicle examples include crewed/uncrewed spacecraft, space station modules, elements, etc. Within this document, any docking space vehicle will be referred to as the host vehicle. This document defines the NDS-to-NDS interfaces, as well as the NDS-to-host vehicle interfaces and performance capability.

  8. GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking.

    Science.gov (United States)

    Weiss, Dahlia R; Bortolato, Andrea; Tehan, Benjamin; Mason, Jonathan S

    2016-04-25

    Virtual screening is routinely used to discover new ligands and in particular new ligand chemotypes for G protein-coupled receptors (GPCRs). To prepare for a virtual screen, we often tailor a docking protocol that will enable us to select the best candidates for further screening. To aid this, we created GPCR-Bench, a publically available docking benchmarking set in the spirit of the DUD and DUD-E reference data sets for validation studies, containing 25 nonredundant high-resolution GPCR costructures with an accompanying set of diverse ligands and computational decoy molecules for each target. Benchmarking sets are often used to compare docking protocols; however, it is important to evaluate docking methods not by "retrospective" hit rates but by the actual likelihood that they will produce novel prospective hits. Therefore, docking protocols must not only rank active molecules highly but also produce good poses that a chemist will select for purchase and screening. Currently, no simple objective machine-scriptable function exists that can do this; instead, docking hit lists must be subjectively examined in a consistent way to compare between docking methods. We present here a case study highlighting considerations we feel are of importance when evaluating a method, intended to be useful as a practitioners' guide. PMID:26958710

  9. Reduced DOCK4 expression leads to erythroid dysplasia in myelodysplastic syndromes.

    Science.gov (United States)

    Sundaravel, Sriram; Duggan, Ryan; Bhagat, Tushar; Ebenezer, David L; Liu, Hui; Yu, Yiting; Bartenstein, Matthias; Unnikrishnan, Madhu; Karmakar, Subhradip; Liu, Ting-Chun; Torregroza, Ingrid; Quenon, Thomas; Anastasi, John; McGraw, Kathy L; Pellagatti, Andrea; Boultwood, Jacqueline; Yajnik, Vijay; Artz, Andrew; Le Beau, Michelle M; Steidl, Ulrich; List, Alan F; Evans, Todd; Verma, Amit; Wickrema, Amittha

    2015-11-17

    Anemia is the predominant clinical manifestation of myelodysplastic syndromes (MDS). Loss or deletion of chromosome 7 is commonly seen in MDS and leads to a poor prognosis. However, the identity of functionally relevant, dysplasia-causing, genes on 7q remains unclear. Dedicator of cytokinesis 4 (DOCK4) is a GTPase exchange factor, and its gene maps to the commonly deleted 7q region. We demonstrate that DOCK4 is underexpressed in MDS bone marrow samples and that the reduced expression is associated with decreased overall survival in patients. We show that depletion of DOCK4 levels leads to erythroid cells with dysplastic morphology both in vivo and in vitro. We established a novel single-cell assay to quantify disrupted F-actin filament network in erythroblasts and demonstrate that reduced expression of DOCK4 leads to disruption of the actin filaments, resulting in erythroid dysplasia that phenocopies the red blood cell (RBC) defects seen in samples from MDS patients. Reexpression of DOCK4 in -7q MDS patient erythroblasts resulted in significant erythropoietic improvements. Mechanisms underlying F-actin disruption revealed that DOCK4 knockdown reduces ras-related C3 botulinum toxin substrate 1 (RAC1) GTPase activation, leading to increased phosphorylation of the actin-stabilizing protein ADDUCIN in MDS samples. These data identify DOCK4 as a putative 7q gene whose reduced expression can lead to erythroid dysplasia. PMID:26578796

  10. Proposed docking interface between peptidoglycan and the target recognition domain of zoocin A

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yinghua [Department of Chemistry, University of Alabama, Tuscaloosa, AL 35487 (United States); Simmonds, Robin S. [Department of Microbiology and Immunology, University of Otago, Dunedin (New Zealand); Timkovich, Russell, E-mail: rtimkovi@bama.ua.edu [Department of Chemistry, University of Alabama, Tuscaloosa, AL 35487 (United States)

    2013-11-15

    Highlights: •Peptidoglycan added to zoocin rTRD perturbs NMR resonances around W115. •Simulations predict docking to a shallow surface groove near W115. •The docking interface is similar to mammalian antibody–antigen sites. •EDTA binds to a distinct surface site. -- Abstract: A docking model is proposed for the target recognition domain of the lytic exoenzyme zoocin A with the peptidoglycan on the outer cell surface of sensitive bacterial strains. Solubilized fragments from such peptidoglycans perturb specific backbone and side chain amide resonances in the recombinant form of the domain designated rTRD as detected in two-dimensional {sup 1}H–{sup 15}N correlation NMR spectra. The affected residues comprise a shallow surface cleft on the protein surface near W115, N53, N117, and Q105 among others, which interacts with the peptide portion of the peptidoglycan. Calculations with AutoDock Vina provide models of the docking interface. There is approximate homology between the rTDR-peptidoglycan docking site and the antigen binding site of Fab antibodies with the immunoglobin fold. EDTA was also found to bind to rTRD, but at a site distinct from the proposed peptidoglycan docking site.

  11. ADMET, Docking studies & binding energy calculations of some Novel ACE - inhibitors for the treatment of Diabetic Nephropathy

    Directory of Open Access Journals (Sweden)

    Gade Deepak Reddy

    2012-09-01

    Full Text Available Diabetic Nephropathy (DN is one of the major complications of diabetes mellitus, representing the leading of cause of chronic renal disease and a major cause of morbidity and mortality in both type 1 and type 2 diabetic patients. The Renin-Angiotensin-Aldosterone System (RAAS has been implicated in the pathophysiology of DN, and suggests a therapeutic target for blocking this system. Therefore, inhibition of RAAS plays a crucial role in the treatment of DN and therapeutic intervention mostly involves administration of angiotensin converting enzyme (ACE inhibitors and angiotensin AT1 receptor blockers. In this current study, we have used computational methods to design 37 novel ACE-inhibitors and evaluated them for the interaction with the enzyme ACE through insilico analysis. The obtained results were compared with the standard drug enalapril to find out the potential inhibitors. Here we report that ligand 4 exhibited strongest inhibitory activity among all. All the analogs are also screened for their ADME & Toxicity profiles using insilico tools and ligand 9 is having better binding affinity next to ligand 4, and also having better ADMET profile when compared to that of ligand 4. Post docking calculations were also performed for the docked complexes in order to identify the individual ligand binding energies by employing Multi-Ligand Bimolecular Association with Energetics (Embrace

  12. Identification of mitogen-activated protein kinase docking sites in enzymes that metabolize phosphatidylinositols and inositol phosphates

    Directory of Open Access Journals (Sweden)

    Buckley Colin T

    2006-01-01

    Full Text Available Abstract Background Reversible interactions between the components of cellular signaling pathways allow for the formation and dissociation of multimolecular complexes with spatial and temporal resolution and, thus, are an important means of integrating multiple signals into a coordinated cellular response. Several mechanisms that underlie these interactions have been identified, including the recognition of specific docking sites, termed a D-domain and FXFP motif, on proteins that bind mitogen-activated protein kinases (MAPKs. We recently found that phosphatidylinositol-specific phospholipase C-γ1 (PLC-γ1 directly binds to extracellular signal-regulated kinase 2 (ERK2, a MAPK, via a D-domain-dependent mechanism. In addition, we identified D-domain sequences in several other PLC isozymes. In the present studies we sought to determine whether MAPK docking sequences could be recognized in other enzymes that metabolize phosphatidylinositols (PIs, as well as in enzymes that metabolize inositol phosphates (IPs. Results We found that several, but not all, of these enzymes contain identifiable D-domain sequences. Further, we found a high degree of conservation of these sequences and their location in human and mouse proteins; notable exceptions were PI 3-kinase C2-γ, PI 4-kinase type IIβ, and inositol polyphosphate 1-phosphatase. Conclusion The results indicate that there may be extensive crosstalk between MAPK signaling and signaling pathways that are regulated by cellular levels of PIs or IPs.

  13. Study on the interaction of the epilepsy drug, zonisamide with human serum albumin (HSA) by spectroscopic and molecular docking techniques

    Science.gov (United States)

    Shahabadi, Nahid; Khorshidi, Aref; Moghadam, Neda Hossinpour

    2013-10-01

    In the present investigation, an attempt has been made to study the interaction of zonisamide (ZNS) with the transport protein, human serum albumin (HSA) employing UV-Vis, fluorometric, circular dichroism (CD) and molecular docking techniques. The results indicated that binding of ZNS to HSA caused strong fluorescence quenching of HSA through static quenching mechanism, hydrogen bonds and van der Waals contacts are the major forces in the stability of protein ZNS complex and the process of the binding of ZNS with HSA was driven by enthalpy (ΔH = -193.442 kJ mol-1). The results of CD and UV-Vis spectroscopy showed that the binding of this drug to HSA induced conformational changes in HSA. Furthermore, the study of molecular docking also indicated that zonisamide could strongly bind to the site I (subdomain IIA) of HSA mainly by hydrophobic interaction and there were hydrogen bond interactions between this drug and HSA, also known as the warfarin binding site.

  14. Insights into the structure and inhibition of Giardia intestinalis arginine deiminase: homology modeling, docking, and molecular dynamics studies.

    Science.gov (United States)

    Trejo-Soto, Pedro Josué; Aguayo-Ortiz, Rodrigo; Yépez-Mulia, Lilián; Hernández-Campos, Alicia; Medina-Franco, José Luis; Castillo, Rafael

    2016-04-01

    Giardia intestinalis arginine deiminase (GiADI) is an important metabolic enzyme involved in the energy production and defense of this protozoan parasite. The lack of this enzyme in the human host makes GiADI an attractive target for drug design against G. intestinalis. One approach in the design of inhibitors of GiADI could be computer-assisted studies of its crystal structure, such as docking; however, the required crystallographic structure of the enzyme still remains unresolved. Because of its relevance, in this work, we present a three-dimensional structure of GiADI obtained from its amino acid sequence using the homology modeling approximation. Furthermore, we present an approximation of the most stable dimeric structure of GiADI identified through molecular dynamics simulation studies. An in silico analysis of druggability using the structure of GiADI was carried out in order to know if it is a good target for design and optimization of selective inhibitors. Potential GiADI inhibitors were identified by docking of a set of 3196 commercial and 19 in-house benzimidazole derivatives, and molecular dynamics simulation studies were used to evaluate the stability of the ligand-enzyme complexes. PMID:26017138

  15. Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

    Science.gov (United States)

    Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

    2016-05-01

    The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. PMID:27060891

  16. Resveratrol inhibits matrix metalloproteinases to attenuate neuronal damage in cerebral ischemia: a molecular docking study exploring possible neuroprotection

    Directory of Open Access Journals (Sweden)

    Anand Kumar Pandey

    2015-01-01

    Full Text Available The main pathophysiology of cerebral ischemia is the structural alteration in the neurovascular unit, coinciding with neurovascular matrix degradation. Resveratrol has been reported to be one of the most potent chemopreventive agents that can inhibit cellular processes associated with ischemic stroke. Matrix metalloproteinases (MMPs has been considered as a potential drug target for the treatment of cerebral ischemia. To explore this, we tried to investigate the interaction of resveratrol with MMPs through molecular docking studies. At 30 minutes before and 2 hours after cerebral ischemia/reperfusion induced by occlusion of the middle cerebral artery, 40 mg/kg resveratrol was intraperitoneally administered. After resveratrol administration, neurological function and brain edema were significantly alleviated, cerebral infarct volume was significantly reduced, and nitrite and malondialdehyde levels in the cortical and striatal regions were significantly decreased. The molecular docking study of resveratrol and MMPs revealed that resveratrol occupied the active site of MMP-2 and MMP-9. The binding energy of the complexes was -37.848672 kJ/mol and -36.6345 kJ/mol for MMP-2 and MMP-9, respectively. In case of MMP-2, Leu 164, Ala 165 and Thr 227 were engaged in H-Bonding with resveratrol and in case of MMP-9, H-bonding was found with Glu 402, Ala 417 and Arg 424 residues. These findings collectively reveal that resveratrol exhibits neuroprotective effects on cerebral ischemia through inhibiting MMP-2 and MMP-9 activity.

  17. GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing.

    Directory of Open Access Journals (Sweden)

    Ye Fang

    Full Text Available Computational modeling of drug binding to proteins is an integral component of direct drug design. Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets. Because of a large number of drug candidates to be evaluated, an accurate and fast docking engine is a critical element of virtual screening. Consequently, highly optimized docking codes are of paramount importance for the effectiveness of virtual screening methods. In this communication, we describe the implementation, tuning and performance characteristics of GeauxDock, a recently developed molecular docking program. GeauxDock is built upon the Monte Carlo algorithm and features a novel scoring function combining physics-based energy terms with statistical and knowledge-based potentials. Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU. First, we carried out a thorough performance tuning of the high-level framework and the docking kernel to produce a fast serial code, which was then ported to shared-memory multi-core CPUs yielding a near-ideal scaling. Further, using Xeon Phi gives 1.9× performance improvement over a dual 10-core Xeon CPU, whereas the best GPU accelerator, GeForce GTX 980, achieves a speedup as high as 3.5×. On that account, GeauxDock can take advantage of modern heterogeneous architectures to considerably accelerate structure-based virtual screening applications. GeauxDock is open-sourced and publicly available at www.brylinski.org/geauxdock and https://figshare.com/articles/geauxdock_tar_gz/3205249.

  18. GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing.

    Science.gov (United States)

    Fang, Ye; Ding, Yun; Feinstein, Wei P; Koppelman, David M; Moreno, Juana; Jarrell, Mark; Ramanujam, J; Brylinski, Michal

    2016-01-01

    Computational modeling of drug binding to proteins is an integral component of direct drug design. Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets. Because of a large number of drug candidates to be evaluated, an accurate and fast docking engine is a critical element of virtual screening. Consequently, highly optimized docking codes are of paramount importance for the effectiveness of virtual screening methods. In this communication, we describe the implementation, tuning and performance characteristics of GeauxDock, a recently developed molecular docking program. GeauxDock is built upon the Monte Carlo algorithm and features a novel scoring function combining physics-based energy terms with statistical and knowledge-based potentials. Developed specifically for heterogeneous computing platforms, the current version of GeauxDock can be deployed on modern, multi-core Central Processing Units (CPUs) as well as massively parallel accelerators, Intel Xeon Phi and NVIDIA Graphics Processing Unit (GPU). First, we carried out a thorough performance tuning of the high-level framework and the docking kernel to produce a fast serial code, which was then ported to shared-memory multi-core CPUs yielding a near-ideal scaling. Further, using Xeon Phi gives 1.9× performance improvement over a dual 10-core Xeon CPU, whereas the best GPU accelerator, GeForce GTX 980, achieves a speedup as high as 3.5×. On that account, GeauxDock can take advantage of modern heterogeneous architectures to considerably accelerate structure-based virtual screening applications. GeauxDock is open-sourced and publicly available at www.brylinski.org/geauxdock and https://figshare.com/articles/geauxdock_tar_gz/3205249. PMID:27420300

  19. Docking System Design and Self-Assembly Control of Distributed Swarm Flying Robots

    Directory of Open Access Journals (Sweden)

    Hongxing Wei

    2012-11-01

    Full Text Available This paper presents a novel docking system design and the distributed self‐assembly control strategy for a Distributed Swarm Flying Robot (DSFR. The DSFR is a swarm robot comprising many identical robot modules that are able to move on the ground, dock with each other and fly coordinately once self‐assembled into a robotic structure. A generalized adjacency matrix method is proposed to describe the configurations of robotic structures. Based on the docking system and the adjacency matrix, experiments are performed to demonstrate and verify the self‐assembly control strategy.

  20. The Dock-in Model of music culture and cross-cultural perception

    OpenAIRE

    Fritz, T.

    2013-01-01

    This paper proposes a model that aims to illustrate how different human music cultures intersect and “dock in” to a set of music features that are universally perceived, while also displaying culture-specific features that must be learned. The model emphasizes that over historic time the music in a given culture can “dock into” and “dock out of” cues that are universally perceived, shifting its potential for cross-cultural perception and interaction. While this model accounts for music ethnol...

  1. JL-2: A Mobile Multi-robot System with Docking and Manipulating Capabilities

    OpenAIRE

    Wei Wang; Wenpeng Yu; Houxiang Zhang

    2010-01-01

    This paper presents a new version of the JL series reconfigurable multi-robot system called JL-2. By virtue of the docking manipulator composed of a parallel mechanism and a cam gripper, every mobile robot in the JL-2 system is able to not only perform tasks in parallel, e.g. moving and grasping, but also dock with each other even if there are large misalignments between two robots. A motorized spherical joint is formed between two docked robots to enhance the locomotion capability of JL-2. T...

  2. HexServer: an FFT-based protein docking server powered by graphics processors

    OpenAIRE

    Macindoe, Gary; Mavridis, Lazaros; Venkatraman, Vishwesh; Devignes, Marie-Dominique; Ritchie, David

    2010-01-01

    HexServer (http://hexserver.loria.fr/) is the first Fourier transform (FFT)-based protein docking server to be powered by graphics processors. Using two graphics processors simultaneously, a typical 6D docking run takes similar to 15 s, which is up to two orders of magnitude faster than conventional FFT-based docking approaches using comparable resolution and scoring functions. The server requires two protein structures in PDB format to be uploaded, and it produces a ranked list of up to 1000...

  3. Vehicle Routing Problem for Fashion Supply Chains with Cross-Docking

    OpenAIRE

    Zhi-Hua Hu; Yingxue Zhao; Tsan-Ming Choi

    2013-01-01

    Cross-docking, as a strategy to reduce lead time and enhance the efficiency of the fashion supply chain, has attracted substantial attention from both the academy and the industry. Cross-docking is a critical part of many fashion and textiles supply chains in practice because it can help to achieve many supply chain strategies such as postponement. We consider a model where there are multiple suppliers and customers in a single cross-docking center. With such a model setting, the issue concer...

  4. Virtual screening of plant derived compounds for aldose reductase inhibition using molecular docking.

    Science.gov (United States)

    Muppalaneni, Naresh Babu; Rao, Allam Appa

    2012-01-01

    The role of the aldose reductase in type 2 diabetes is widely described. Therefore, it is of interest to identify plant derived compounds to inhibit its activity. We studied the protein-ligand interaction of 267 compounds from different parts of seven plants (Allium sativum, Coriandrum sativum, Dacus carota, Murrayyakoneigii, Eucalyptus, Calendula officinalis and Lycopersicon esculentum) with aldose reductase as the target protein. Molecular docking and re-scoring of top ten compounds (using GOLD, AutoDock Vina, eHiTS, PatchDock and MEDock) followed by rank-sum technique identified compound allium38 with high binding affinity for aldose reductase. PMID:23275691

  5. Nuclear physicist, arms control advocate

    CERN Multimedia

    Chang, K

    2002-01-01

    Victor F. Weisskopf, a nuclear physicist who worked on the Manhattan Project to build the first atomic bomb in World War II and later became an ardent advocate of arms control, died Monday at his home in Newton, MA, USA. He was 93 (1 page).

  6. Rhetorical Histories and Arms Negotiations.

    Science.gov (United States)

    Kane, Thomas

    1988-01-01

    Argues that the use of historical events as rhetorical artifacts has sustained cold war assumptions and attitudes; that rhetorical events provide composites for rhetorical histories which become the basis for argumentative appeals; and that these rhetorical histories continue to permeate American diplomacy in general and arms negotiations in…

  7. Elucidating the binding efficacy of β-galactosidase on graphene by docking approach and its potential application in galacto-oligosaccharide production.

    Science.gov (United States)

    Satar, Rukhsana; Ismail, Syed Ahmed; Rehan, Mohd; Ansari, Shakeel Ahmed

    2016-05-01

    Herein, we propose the synthesis and characterization of graphene for the immobilization of β-galactosidase for improved galacto-oligosaccharide (GOS) production. The size of synthesized graphene was observed to be 25 nm by TEM analysis while interaction of enzyme with the nanosupport was observed by FTIR spectroscopy. Docking was obtained using molecular docking program Dock v.6.5 while the visual analyses and illustration of protein-ligand complex were investigated by utilizing chimera v.1.6.2 and PyMOL v.1.3 softwares. Immobilized β-galactosidase (IβG) showed improved stability against various physical and chemical denaturants. K m of IβG was increased to 6.41 mM as compared to 2.38 mM of soluble enzyme without bringing significant change in V max value. Maximum GOS content also registered an increase in lactose conversion. The maximum GOS production was achieved by immobilized enzyme at specific temperature and time. Hence, the developed nanosupport can be further exploited for developing a biosensor involving β-galactosidase or for immobilization of other industrially/therapeutically important enzymes. PMID:26861556

  8. 33 CFR 154.510 - Loading arms.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Loading arms. 154.510 Section 154... FACILITIES TRANSFERRING OIL OR HAZARDOUS MATERIAL IN BULK Equipment Requirements § 154.510 Loading arms. (a) Each mechanical loading arm used for transferring oil or hazardous material and placed into...

  9. 32 CFR 935.134 - Arm signals.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Arm signals. 935.134 Section 935.134 National... WAKE ISLAND CODE Motor Vehicle Code § 935.134 Arm signals. (a) Any person operating a motor vehicle and... signal for a turn or stop is made by fully extending the left arm as follows: (1) Left turn—extend...

  10. Performance of arm locking in LISA

    Science.gov (United States)

    McKenzie, Kirk; Spero, Robert E.; Shaddock, Daniel A.

    2009-11-01

    For the Laser Interferometer Space Antenna (LISA) to reach its design sensitivity, the coupling of the free-running laser frequency noise to the signal readout must be reduced by more than 14 orders of magnitude. One technique employed to reduce the laser frequency noise will be arm locking, where the laser frequency is locked to the LISA arm length. In this paper we detail an implementation of arm locking. We investigate orbital effects (changing arm lengths and Doppler frequencies), the impact of errors in the Doppler knowledge that can cause pulling of the laser frequency, and the noise limit of arm locking. Laser frequency pulling is examined in two regimes: at lock acquisition and in steady state. The noise performance of arm locking is calculated with the inclusion of the dominant expected noise sources: ultrastable oscillator (clock) noise, spacecraft motion, and shot noise. We find that clock noise and spacecraft motion limit the performance of dual arm locking in the LISA science band. Studying these issues reveals that although dual arm locking [A. Sutton and D. A. Shaddock, Phys. Rev. DPRVDAQ1550-7998 78, 082001 (2008)10.1103/PhysRevD.78.082001] has advantages over single (or common) arm locking in terms of allowing high gain, it has disadvantages in both laser frequency pulling and noise performance. We address this by proposing a modification to the dual arm-locking sensor, a hybrid of common and dual arm-locking sensors. This modified dual arm-locking sensor has the laser frequency pulling characteristics and low-frequency noise coupling of common arm locking, but retains the control system advantages of dual arm locking. We present a detailed design of an arm-locking controller and perform an analysis of the expected performance when used with and without laser prestabilization. We observe that the sensor phase changes beneficially near unity-gain frequencies of the arm-locking controller, allowing a factor of 10 more gain than previously believed

  11. Inhibitor designing, virtual screening, and docking studies for methyltransferase: A potential target against dengue virus

    Science.gov (United States)

    Singh, Jagbir; Kumar, Mahesh; Mansuri, Rani; Sahoo, Ganesh Chandra; Deep, Aakash

    2016-01-01

    Aim: Aim of this work was to design and identify some S-adenosyl-L-homocysteine (SAH) analogs as inhibitors of S-adenosyl-L-methionine-dependent methyltransferase (MTase) protein using computational approaches. Introduction: According to the current scenario the dengue has been a global burden. The people are being killed by dengue virus in an abundant number. Despite of lot of research being going on dengue worldwide, there is no single drug which can kill its virus. This creates an urge for new drug target identification and designing. MTase has been reported as an effective target against dengue virus as it catalyzes an essential step in methylation and capping of viral RNA for viral replication. Materials and Methods: The crystal structure of MTase in complex with SAH was used for designing new analogs of SAH. SAH analogs designed were analyzed on the basis of docking, ADMET, and toxicity analysis done using Discovery Studio 3.5. Results: Seventeen analogs found noncarcinogenic, nonmutagenic, as well as good ADMET properties and good drug-like profile. Conclusion: These SAH analogs, inhibitors of MTase may act as drugs against dengue virus. Further synthesis and biological testing against dengue virus is under observation. PMID:27413346

  12. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies.

    Science.gov (United States)

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper. PMID:27089183

  13. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies

    Science.gov (United States)

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298 K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper.

  14. pK(a) based protonation states and microspecies for protein-ligand docking.

    Science.gov (United States)

    ten Brink, Tim; Exner, Thomas E

    2010-11-01

    In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein-ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein-Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach. PMID:20882397

  15. Interaction study of ciprofloxacin with human telomeric DNA by spectroscopy and molecular docking

    Science.gov (United States)

    Li, Huihui; Bu, Xiaoyang; Lu, Jia; Xu, Chongzheng; Wang, Xianlong; Yang, Xiaodi

    2013-04-01

    The interaction of ciprofloxacin (CIP) with human telomeric DNA was studied in vitro using multi-spectroscopy and molecular modeling methods. The hypochromic effect with a red shift in ultraviolet (UV) absorption indicated the occurrence of the interaction between CIP and DNA. The fluorescence quenching of CIP was observed with the addition of DNA and was proved to be the static quenching. The binding constant was found to be 9.62 × 104 L mol-1. Electrospray ionization mass spectrometry (ESI-MS) result further confirmed the formation of 1:1 non-covalent complex between DNA and CIP. Combined with the UV melting results, circular dichroism (CD) results confirmed the existence of groove binding mode, as well as conformational changes of DNA. Molecular docking studies illustrated the visual display of the CIP binding to the GC region in the minor groove of DNA. Specific hydrogen bonds and van der Waals forces were demonstrated as main acting forces between CIP and guanine bases of DNA.

  16. [A case of Creutzfeldt-Jakob disease presenting with arm levitation as an initial symptom].

    Science.gov (United States)

    Kamogawa, Kenji; Ninomiya, Satoko; Okuda, Shinya; Matsumoto, Yushi; Tomita, Hitomi; Okamoto, Kensho; Okuda, Bungo

    2014-01-01

    A 74-year-old, right handed man, developed insidiously with levitation and clumsiness of the right upper limb. His right arm tended to levitate spontaneously, when he was examined. He could put the elevated arm down on command, while the arm resumed to antigravity posture when his attention was diverted. His right arm also exhibited unwilled elevation when performing complex finger movements on the right side. He had a feeling of strangeness of the elevated limb, especially with the eyes closed. In addition to asymmetric limb-kinetic apraxia, combined sensations such as stereognosis were disturbed on the right side. Brain MRI showed high signal lesions predominantly in the left cerebral cortices and basal ganglia. SPECT with (123)I-IMP revealed asymmetric hypoperfusion, predominantly in the left medial frontal and parietal regions. Two months after the onset, levitation of the arm gradually disappeared, with the development of rapidly progressive dementia, frontal signs, dystonia and generalized myoclonus. The diagnosis of Creutzfeldt-Jakob disease (CJD) was made based on the clinical features and cerebrospinal fluid biomarkers. The early manifestation of the patient mimicked corticobasal degeneration which presents with arm levitation or alien hand syndrome. It is suggested that CJD can represent involuntary movements with higher brain dysfunction resembling corticobasal degeneration at the early stage of the illness. Although the underlying mechanism of arm levitation is still unknown, frontal disinhibition and parietal cortical sensory disturbance may contribute to the development of involuntary arm levitation in our patient. PMID:25342014

  17. Interaction of bovine serum albumin with a psychotropic drug alprazolam: Physicochemical, photophysical and molecular docking studies

    International Nuclear Information System (INIS)

    The interaction between alprazolam (Alp) and bovine serum albumin (BSA) has been investigated under physiological conditions by UV–vis, steady state as well as time-resolved fluorescence, circular dichroism (CD) spectroscopic and molecular docking studies. The binding constant K of Alp to BSA was found to be 1.8×105 L mol−1 from absorption data. Fluorometric studies suggested the formation of the Alp–BSA complex, while time-resolved fluorescence studies showed that the binding of Alp by BSA was mainly static and the effective rate constant is found to be 2.33×1013 L mol−1 s−1. According to the modified Stern–Volmer equation, the Stern–Volmer quenching constants (KSV) between Alp and BSA at four different temperatures 295, 303, 308, 313 K were obtained to be 1.19×105, 1.05×105, 0.99×105 and 0.90×105 L mol−1, respectively. The change in enthalpy (ΔH) and entropy (ΔS) were calculated to be −11.66 and 57.64 J mol−1 K−1, respectively, indicating that the interaction was hydrophobic in nature. Site marker competitive experiments suggested that the binding of Alp to BSA primarily took place in sub-domain IIA, whereas the binding distance (r) between Alp and the tryptophan residue of BSA was obtained to be 1.87 nm by Förster's theory of non-radiative energy transfer. The conformational studies by CD spectroscopy showed that the presence of Alp decreased the α-helical content of BSA and induced the unfolding of the polypeptide of the protein. The change in conformation was also supported by excitation–emission matrix spectroscopy (EEMS) studies. The molecular docking experiment supports the above results and effectively proves the binding of Alp to BSA. -- Highlights: • Alprazolam: a benzodiazepine drug with anxiolytic and anticonvulsant properties. • Alprazolam induces conformational change on the native as well as urea denatured BSA. • Alprazolam may interfere with serum albumin function in the long run

  18. Interaction of bovine serum albumin with a psychotropic drug alprazolam: Physicochemical, photophysical and molecular docking studies

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Moumita; Paul, Shiv Shankar; Mukherjea, Kalyan K., E-mail: k_mukherjea@yahoo.com

    2013-10-15

    The interaction between alprazolam (Alp) and bovine serum albumin (BSA) has been investigated under physiological conditions by UV–vis, steady state as well as time-resolved fluorescence, circular dichroism (CD) spectroscopic and molecular docking studies. The binding constant K of Alp to BSA was found to be 1.8×10{sup 5} L mol{sup −1} from absorption data. Fluorometric studies suggested the formation of the Alp–BSA complex, while time-resolved fluorescence studies showed that the binding of Alp by BSA was mainly static and the effective rate constant is found to be 2.33×10{sup 13} L mol{sup −1} s{sup −1}. According to the modified Stern–Volmer equation, the Stern–Volmer quenching constants (K{sub SV}) between Alp and BSA at four different temperatures 295, 303, 308, 313 K were obtained to be 1.19×10{sup 5}, 1.05×10{sup 5}, 0.99×10{sup 5} and 0.90×10{sup 5} L mol{sup −1}, respectively. The change in enthalpy (ΔH) and entropy (ΔS) were calculated to be −11.66 and 57.64 J mol{sup −1} K{sup −1}, respectively, indicating that the interaction was hydrophobic in nature. Site marker competitive experiments suggested that the binding of Alp to BSA primarily took place in sub-domain IIA, whereas the binding distance (r) between Alp and the tryptophan residue of BSA was obtained to be 1.87 nm by Förster's theory of non-radiative energy transfer. The conformational studies by CD spectroscopy showed that the presence of Alp decreased the α-helical content of BSA and induced the unfolding of the polypeptide of the protein. The change in conformation was also supported by excitation–emission matrix spectroscopy (EEMS) studies. The molecular docking experiment supports the above results and effectively proves the binding of Alp to BSA. -- Highlights: • Alprazolam: a benzodiazepine drug with anxiolytic and anticonvulsant properties. • Alprazolam induces conformational change on the native as well as urea denatured BSA. • Alprazolam may

  19. Docks and Piers, Fishing Piers in, Published in unknown, Manatee County Information Services Dept..

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Docks and Piers dataset as of unknown. It is described as 'Fishing Piers in'. Data by this publisher are often provided in State Plane coordinate system; in a...

  20. A Ground Testbed to Advance US Capability in Autonomous Rendezvous and Docking Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The entire Agency supports development of a Commodity for Autonomous Rendezvous and Docking (CARD) as outlined in the Agency-wide Community of Practice whitepaper...

  1. Actin- and Myosin-Dependent Vesicle Loading of Presynaptic Docking Sites Prior to Exocytosis.

    Science.gov (United States)

    Miki, Takafumi; Malagon, Gerardo; Pulido, Camila; Llano, Isabel; Neher, Erwin; Marty, Alain

    2016-08-17

    Variance analysis of postsynaptic current amplitudes suggests the presence of distinct docking sites (also called release sites) where vesicles pause before exocytosis. Docked vesicles participate in the readily releasable pool (RRP), but the relation between docking site number and RRP size remains unclear. It is also unclear whether all vesicles of the RRP are equally release competent, and what cellular mechanisms underlie RRP renewal. We address here these questions at single glutamatergic synapses, counting released vesicles using deconvolution. We find a remarkably low variance of cumulative vesicle counts during action potential trains. This, combined with Monte Carlo simulations, indicates that vesicles transit through two successive states before exocytosis, so that the RRP is up to 2-fold higher than the docking site number. The transition to the second state has a very rapid rate constant, and is specifically inhibited by latrunculin B and blebbistatin, suggesting the involvement of actin and myosin. PMID:27537485

  2. JL-2: A Mobile Multi-robot System with Docking and Manipulating Capabilities

    Directory of Open Access Journals (Sweden)

    Wei Wang

    2010-02-01

    Full Text Available This paper presents a new version of the JL series reconfigurable multi-robot system called JL-2. By virtue of the docking manipulator composed of a parallel mechanism and a cam gripper, every mobile robot in the JL-2 system is able to not only perform tasks in parallel, e.g. moving and grasping, but also dock with each other even if there are large misalignments between two robots. A motorized spherical joint is formed between two docked robots to enhance the locomotion capability of JL-2. To fulfill the demands of reconfiguration, a distributed control system and sonar based docking guidance system are designed for the JL-2 prototype. Based on the above design, the JL-2 prototype has been built and successfully demonstrated to confirm the validity and functionality of the proposed capabilities.

  3. A biologically inspired neural network controller for ballistic arm movements

    OpenAIRE

    Schmid Maurizio; Accornero Neri; Capozza Marco; Conforto Silvia; Bernabucci Ivan; D'Alessio Tommaso

    2007-01-01

    Abstract Background In humans, the implementation of multijoint tasks of the arm implies a highly complex integration of sensory information, sensorimotor transformations and motor planning. Computational models can be profitably used to better understand the mechanisms sub-serving motor control, thus providing useful perspectives and investigating different control hypotheses. To this purpose, the use of Artificial Neural Networks has been proposed to represent and interpret the movement of ...

  4. Cultural methods for controlling docks in organically farmed grassland (extension 1998-99) (OFT0115T)

    OpenAIRE

    Hopkins, Alan

    1999-01-01

    Docks are considered to be one of the main weed problems of grassland. The absence of an effective non-chemical control may be a deterrent to organic-conversion for farmers accustomed to using herbicides for dock control. This work addresses this problem in the context of MAFF policy to encourage more farmers to adopt organic farming, and to encourage a reduction in the use of herbicides in farming generally. The project was based around hypotheses that physical techniques and management stra...

  5. ASTP crewmen in Docking Module trainer during training session at JSC

    Science.gov (United States)

    1975-01-01

    An interior view of the Docking Module trainer in bldg 35 during Apollo Soyuz Test Project (ASTP) joint crew training at JSC. Astronaut Thomas P. Stafford, commander of the American ASTP prime crew, is on the right. The other crewman is Cosmonaut Aleksey A. Leonov, commander of the Soviet ASTP prime crew. The training session simulated activities on the second day in Earth orbit. The Docking Module is designed to link the Apollo and Soyuz spacecraft.

  6. Automatic Docking System with Recharging and Battery Replacement for Surveillance Robot

    OpenAIRE

    M. Meena; Mrs. P. Thilagavathi*

    2012-01-01

    Most of the applications like industrial automation, home automation, hospitals, space exploration, military, etc, the surveillance robot are widely used. For that, continuous functioning of surveillance robot is necessary. In this paper, the development of automatic docking system with recharging and battery replacement process for surveillance robot is proposed. The robot can return to the docking station for recharging operations when the battery is low. The charging duration of the batter...

  7. International Low Impact Docking System (iLIDS) Project Technical Requirements Specification, Revision F

    Science.gov (United States)

    Lewis, James L.

    2011-01-01

    The NASA Docking System (NDS) is NASA's implementation for the emerging International Docking System Standard (IDSS) using low impact docking technology. The NASA Docking System Project (NDSP) is the International Space Station (ISS) Program's project to produce the NDS, Common Docking Adapter (CDA) and Docking Hub. The NDS design evolved from the Low Impact Docking System (LIDS). The acronym international Low Impact Docking System (iLIDS) is also used to describe this system as well as the Government Furnished Equipment (GFE) project designing the NDS for the NDSP. NDS and iLIDS may be used interchangeability. This document will use the acronym iLIDS. Some of the heritage documentation and implementations (e.g., software command names, requirement identification (ID), figures, etc.) used on NDS will continue to use the LIDS acronym. This specification defines the technical requirements for the iLIDS GFE delivered to the NDSP by the iLIDS project. This document contains requirements for two iLIDS configurations, SEZ29101800-301 and SEZ29101800-302. Requirements with the statement, iLIDS shall, are for all configurations. Examples of requirements that are unique to a single configuration may be identified as iLIDS (-301) shall or iLIDS (-302) shall. Furthermore, to allow a requirement to encompass all configurations with an exception, the requirement may be designated as iLIDS (excluding -302) shall. Verification requirements for the iLIDS project are identified in the Verification Matrix (VM) provided in the iLIDS Verification and Validation Document, JSC-63966. The following definitions differentiate between requirements and other statements: Shall: This is the only verb used for the binding requirements. Should/May: These verbs are used for stating non-mandatory goals. Will: This verb is used for stating facts or declaration of purpose. A Definition of Terms table is provided in Appendix B to define those terms with specific tailored uses in this document.

  8. Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration.

    OpenAIRE

    Grimsley, C M; Kinchen, J M; Tosello-Trampont, A C; Brugnera, E.; Haney, L B; Lu, M; Chen, Q.; Klingele, D; Hengartner, M O; K.S.Ravichandran

    2004-01-01

    Cell migration is essential throughout embryonic and adult life. In numerous cell systems, the small GTPase Rac is required for lamellipodia formation at the leading edge and movement ability. However, the molecular mechanisms leading to Rac activation during migration are still unclear. Recently, a mammalian superfamily of proteins related to the prototype member Dock180 has been identified with homologues in Drosophila and Caenorhabditis elegans. Here, we addressed the role of Dock180 and E...

  9. Automated waste canister docking and emplacement using a sensor-based intelligent controller

    International Nuclear Information System (INIS)

    A sensor-based intelligent control system is described that utilizes a multiple degree-of-freedom robotic system for the automated remote manipulation and precision docking of large payloads such as waste canisters. Computer vision and ultrasonic proximity sensing are used to control the automated precision docking of a large object with a passive target cavity. Real-time sensor processing and model-based analysis are used to control payload position to a precision of ± 0.5 millimeter

  10. Situation Awareness for Improved Operational Control in Cross Docking: An Illustrative Case Study

    OpenAIRE

    Buijs, Paul; Szirbik, Nick; Meyer, Gerben; Wortmann, Johan

    2012-01-01

    This paper presents research in progress aimed at developing a conceptual framework for operational control at cross docks. The proposed framework contributes to cross docking literature by including situation awareness as an important concept of operational control. The implications of the proposed conceptual framework are explored in an illustrative case study. That case study reveals that despite the availability of real-time and detailed information about the on-going operations, the abil...

  11. Integrating atom-based and residue-based scoring functions for protein–protein docking

    OpenAIRE

    Vreven, Thom; Hwang, Howook; Weng, Zhiping

    2011-01-01

    Most scoring functions for protein–protein docking algorithms are either atom-based or residue-based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom-based terms. Here we combine ZRANK's atom-based potentials with five residue-based potentials published by other labs, as well as an atom-ba...

  12. A polynomial algorithm for a simple scheduling problem at cross docking terminals

    OpenAIRE

    Sadykov, Ruslan

    2009-01-01

    At cross docking terminals, products from incoming trucks are sorted according to there destinations and transferred to outgoing trucks using a temporary storage. Such terminals allow companies to reduce storage and transportation costs in supply chain. This paper focuses on the operational activities at cross docking terminals. We consider the trucks scheduling problem with the objective to minimise the storage usage during the product transfer. We show that a simplification of this NP-hard ...

  13. A New Method for Ligand Docking to Flexible Receptors by Dual Alanine Scanning and Refinement (SCARE)

    OpenAIRE

    Bottegoni, Giovanni; Kufareva, Irina; Totrov, Maxim; Abagyan, Ruben

    2008-01-01

    Protein binding sites undergo ligand specific conformational changes upon ligand binding. However, most docking protocols rely on a fixed conformation of the receptor, or on the prior knowledge of multiple conformations representing the variation of the pocket, or on a known bounding box for the ligand. Here we described a general induced fit docking protocol that requires only one initial pocket conformation and identifies most of the correct ligand positions as the lowest score. We expanded...

  14. A Multiobjective Iterated Greedy Algorithm for Truck Scheduling in Cross-Dock Problems

    OpenAIRE

    B. Naderi; Shadi Rahmani; Shabnam Rahmani

    2014-01-01

    The cross-docking system is a new distribution strategy which can reduce inventories, lead times, and improve responding time to customers. This paper considers biobjective problem of truck scheduling in cross-docking systems with temporary storage. The objectives are minimizing both makespan and total tardiness. For this problem, it proposes a multiobjective iterated greedy algorithm employing advance features such as modified crowding selection, restart phase, and local search. To evaluate ...

  15. Consistent improvement of cross docking results using binding site ensembles generated with Elastic Network Normal Modes

    OpenAIRE

    Rueda, Manuel; Bottegoni, Giovanni; Abagyan, Ruben

    2009-01-01

    The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article we use a large and diverse benchmark to prove that is possible to improve consistently the cross docking performance against a single receptor conformation by using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and the top ranked near native poses for the ligand were found 20% more efficiently than using a single ...

  16. Identification of Novel Smoothened Ligands Using Structure-Based Docking

    Science.gov (United States)

    Torosyan, Hayarpi; Parathaman, Pranavan; Irwin, John J.; Shoichet, Brian K.

    2016-01-01

    The seven transmembrane protein Smoothened is required for Hedgehog signaling during embryonic development and adult tissue homeostasis. Inappropriate activation of the Hedgehog signalling pathway leads to cancers such as basal cell carcinoma and medulloblastoma, and Smoothened inhibitors are now available clinically to treat these diseases. However, resistance to these inhibitors rapidly develops thereby limiting their efficacy. The determination of Smoothened crystal structures enables structure-based discovery of new ligands with new chemotypes that will be critical to combat resistance. In this study, we docked 3.2 million available, lead-like molecules against Smoothened, looking for those with high physical complementarity to its structure; this represents the first such campaign against the class Frizzled G-protein coupled receptor family. Twenty-one high-ranking compounds were selected for experimental testing, and four, representing three different chemotypes, were identified to antagonize Smoothened with IC50 values better than 50 μM. A screen for analogs revealed another six molecules, with IC50 values in the low micromolar range. Importantly, one of the most active of the new antagonists continued to be efficacious at the D473H mutant of Smoothened, which confers clinical resistance to the antagonist vismodegib in cancer treatment. PMID:27490099

  17. Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

    Directory of Open Access Journals (Sweden)

    Renata De Paris

    2015-01-01

    Full Text Available Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

  18. Reducing Seal Adhesion in Low Impact Docking Systems

    Science.gov (United States)

    Banks, Bruce A.; Miller, Sharon K.

    2010-01-01

    Silicone elastomers, used in seals for airlocks or other sealing surfaces in space, are sticky in their as-received condition. Because of the sticking, a greater force may be needed to separate the mating surfaces. If the adhesion is sufficiently high, a sudden unpredicted movement of the spacecraft during undocking, vibration, or uneven release could pull off the seal, resulting in a damage that would have to be repaired before another docking. The damaged seal can result in significant gas leakage and possibly in a catastrophic mishap impacting the safety of the crew. It is also possible that a compromised seal could result in a delayed but sudden gas leak that could put the crew at unexpected risk. This is especially of concern for androgynous seals, which have identical mating surfaces on both sides for interchangeability and redundancy. Such seals typically have elastomer-on-elastomer sealing surfaces. To reduce sticking, one could use release agents such as powders and lubricants, but these can be easily removed and transferred to other surfaces, causing uneven sealing and contamination. Modification of the elastomer surface to make a more slippery and less sticky surface that is integral with the bulk elastomer would be more desirable.

  19. Noncatalytic docking domains of cellulosomes of anaerobic fungi.

    Science.gov (United States)

    Steenbakkers, P J; Li, X L; Ximenes, E A; Arts, J G; Chen, H; Ljungdahl, L G; Op Den Camp, H J

    2001-09-01

    A method is presented for the specific isolation of genes encoding cellulosome components from anaerobic fungi. The catalytic components of the cellulosome of anaerobic fungi typically contain, besides the catalytic domain, mostly two copies of a 40-amino-acid cysteine-rich, noncatalytic docking domain (NCDD) interspaced by short linkers. Degenerate primers were designed to anneal to the highly conserved region within the NCDDs of the monocentric fungus Piromyces sp. strain E2 and the polycentric fungus Orpinomyces sp. strain PC-2. Through PCR using cDNA from Orpinomyces sp. and genomic DNA from Piromyces sp. as templates, respectively, 9 and 19 PCR products were isolated encoding novel NCDD linker sequences. Screening of an Orpinomyces sp. cDNA library with four of these PCR products resulted in the isolation of new genes encoding cellulosome components. An alignment of the partial NCDD sequence information obtained and an alignment of database-accessible NCDD sequences, focusing on the number and position of cysteine residues, indicated the presence of three structural subfamilies within fungal NCDDs. Furthermore, evidence is presented that the NCDDs in CelC from the polycentric fungus Orpinomyces sp. strain PC-2 specifically recognize four proteins in a cellulosome preparation, indicating the presence of multiple scaffoldins. PMID:11514516

  20. Peptides Trapping Dioxins: A Docking-Based Inverse Screening Approach

    Directory of Open Access Journals (Sweden)

    German Perez

    2013-01-01

    Full Text Available A rapid and cost-effective computational methodology for designing and rationalizing the selection of small peptides as receptors for dioxin-like compounds was proposed. The backbone of the dioxin Ah receptor binding site was used to design a series of penta- and hexapeptide libraries, with 1400 elements in total. Peptide flexibility was considered and 10 conformers were found to be a good option to represent peptide conformational space with fair speed-accuracy ratio. Each peptide conformer was treated as a possible receptor, generating a dedicated box and then running a docking process using as ligands a family of 76 dibenzo-p-dioxins and 113 dibenzofurans mono- and polychlorinated. Significant predictions were confirmed by comparing primary structure of top and bottom ranked peptides binding dioxins confirming that scrambled positions of the same amino acids gave completely different predicted binding. The hexapeptide EWFQPW, with the best binding score, was chosen as selective sorbent material in solid-phase extraction. The retention performances were tested using the 2,3,7,8-tetrachlorodibenzo-p-dioxin and two polychlorinated biphenyls in order to verify the hexapeptide specificity. The solid-phase extraction experimental procedure was optimized, and analytical parameters of hexapeptide sorbent material were compared with the resin without hexapeptide and a commercial reversed phase cartridge.