WorldWideScience

Sample records for antibody-antigen docking compensates

  1. Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

    Science.gov (United States)

    Akiba, Hiroki; Tsumoto, Kouhei

    2015-07-01

    Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity.

  2. Control of antibody-antigen binding or dissociation by electric field

    Science.gov (United States)

    Oldham, Philip B.; Asanov, Alexander N.

    1999-04-01

    The development of a biosensor with adequate sensitivity generally requires a biospecific interaction with high binding affinity. The affinity constants for most antibody- antigen interactions are determined largely by the dissociation constants, kd, with little variation observed in rates of associated. additionally, surface immobilization typically results in a reduced kd. In this case, the sensor binds analyte kinetically irreversibly preventing response to changes in analytic concentration or reuse. Regeneration of the sensor surface is difficult, at best. On the other hand, a higher dissociation rate which would lend itself to a linear and reusable sensor, results in lower affinity and poor sensitivity. Consequently, most biosensors are disposable devices and quantitation is obtained using multiple single-use sensors. In this work, a new reusable biosensor platform which provides simultaneous fluorescence detection and electrochemical control of biospecific binding has been developed. Biotin was covalently attached to a transparent indium tin oxide electrode, which also served as an integral part of a total internal reflection fluorescence (TIRF) flow cell. TIRF was used to monitor biospecific interactions while electrochemical polarization was employed to control the interactions. Two possible mechanisms of the electric field effect involving interactions with induced and permanent dipoles of proteins will be discussed.

  3. Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.

    Science.gov (United States)

    Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O

    2016-07-25

    Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation. PMID:27367467

  4. Multiscale sensing of antibody-antigen interactions by organic transistors and single-molecule force spectroscopy.

    Science.gov (United States)

    Casalini, Stefano; Dumitru, Andra C; Leonardi, Francesca; Bortolotti, Carlo A; Herruzo, Elena T; Campana, Alessandra; de Oliveira, Rafael F; Cramer, Tobias; Garcia, Ricardo; Biscarini, Fabio

    2015-05-26

    Antibody-antigen (Ab-Ag) recognition is the primary event at the basis of many biosensing platforms. In label-free biosensors, these events occurring at solid-liquid interfaces are complex and often difficult to control technologically across the smallest length scales down to the molecular scale. Here a molecular-scale technique, such as single-molecule force spectroscopy, is performed across areas of a real electrode functionalized for the immunodetection of an inflammatory cytokine, viz. interleukin-4 (IL4). The statistical analysis of force-distance curves allows us to quantify the probability, the characteristic length scales, the adhesion energy, and the time scales of specific recognition. These results enable us to rationalize the response of an electrolyte-gated organic field-effect transistor (EGOFET) operated as an IL4 immunosensor. Two different strategies for the immobilization of IL4 antibodies on the Au gate electrode have been compared: antibodies are bound to (i) a smooth film of His-tagged protein G (PG)/Au; (ii) a 6-aminohexanethiol (HSC6NH2) self-assembled monolayer on Au through glutaraldehyde. The most sensitive EGOFET (concentration minimum detection level down to 5 nM of IL4) is obtained with the first functionalization strategy. This result is correlated to the highest probability (30%) of specific binding events detected by force spectroscopy on Ab/PG/Au electrodes, compared to 10% probability on electrodes with the second functionalization. Specifically, this demonstrates that Ab/PG/Au yields the largest areal density of oriented antibodies available for recognition. More in general, this work shows that specific recognition events in multiscale biosensors can be assessed, quantified, and optimized by means of a nanoscale technique. PMID:25868724

  5. Characterisation of peptide microarrays for studying antibody-antigen binding using surface plasmon resonance imagery.

    Directory of Open Access Journals (Sweden)

    Claude Nogues

    Full Text Available BACKGROUND: Non-specific binding to biosensor surfaces is a major obstacle to quantitative analysis of selective retention of analytes at immobilized target molecules. Although a range of chemical antifouling monolayers has been developed to address this problem, many macromolecular interactions still remain refractory to analysis due to the prevalent high degree of non-specific binding. We describe how we use the dynamic process of the formation of self assembling monolayers and optimise physical and chemical properties thus reducing considerably non-specific binding and allowing analysis of specific binding of analytes to immobilized target molecules. METHODOLOGY/PRINCIPAL FINDINGS: We illustrate this approach by the production of specific protein arrays for the analysis of interactions between the 65kDa isoform of human glutamate decarboxylase (GAD65 and a human monoclonal antibody. Our data illustrate that we have effectively eliminated non-specific interactions with the surface containing the immobilised GAD65 molecules. The findings have several implications. First, this approach obviates the dubious process of background subtraction and gives access to more accurate kinetic and equilibrium values that are no longer contaminated by multiphase non-specific binding. Second, an enhanced signal to noise ratio increases not only the sensitivity but also confidence in the use of SPR to generate kinetic constants that may then be inserted into van't Hoff type analyses to provide comparative DeltaG, DeltaS and DeltaH values, making this an efficient, rapid and competitive alternative to ITC measurements used in drug and macromolecular-interaction mechanistic studies. Third, the accuracy of the measurements allows the application of more intricate interaction models than simple Langmuir monophasic binding. CONCLUSIONS: The detection and measurement of antibody binding by the type 1 diabetes autoantigen GAD65 represents an example of an antibody-antigen

  6. Antibody-antigen-adjuvant conjugates enable co-delivery of antigen and adjuvant to dendritic cells in cis but only have partial targeting specificity

    NARCIS (Netherlands)

    Kreutz, M.; Giquel, B.; Hu, Q.; Abuknesha, R.; Uematsu, S.; Akira, S.; Nestle, F.O.; Diebold, S.S.

    2012-01-01

    Antibody-antigen conjugates, which promote antigen-presentation by dendritic cells (DC) by means of targeted delivery of antigen to particular DC subsets, represent a powerful vaccination approach. To ensure immunity rather than tolerance induction the co-administration of a suitable adjuvant is par

  7. Effect of polyethylene glycol conjugation on conformational and colloidal stability of a monoclonal antibody antigen-binding fragment (Fab').

    Science.gov (United States)

    Roque, Cristopher; Sheung, Anthony; Rahman, Nausheen; Ausar, S Fernando

    2015-02-01

    We have investigated the effects of site specific "hinge" polyethylene glycol conjugation (PEGylation) on thermal, pH, and colloidal stability of a monoclonal antibody antigen-binding fragment (Fab') using a variety of biophysical techniques. The results obtained by circular dichroism (CD), ultraviolet (UV) absorbance, and fluorescence spectroscopy suggested that the physical stability of the Fab' is maximized at pH 6-7 with no apparent differences due to PEGylation. Temperature-induced aggregation experiments revealed that PEGylation was able to increase the transition temperature, as well as prevent the formation of visible and subvisible aggregates. Statistical comparison of the three-index empirical phase diagram (EPD) revealed significant differences in thermal and pH stability signatures between Fab' and PEG-Fab'. Upon mechanical stress, micro-flow imaging (MFI) and measurement of the optical density at 360 nm showed that the PEG-Fab' had significantly higher resistance to surface-induced aggregation compared to the Fab'. Analysis of the interaction parameter, kD, indicated repulsive intermolecular forces for PEG-Fab' and attractive forces for Fab'. In conclusion, PEGylation appears to protect Fab' against thermal and mechanical stress-induced aggregation, likely due to a steric hindrance mechanism.

  8. Antibody-antigen-adjuvant conjugates enable co-delivery of antigen and adjuvant to dendritic cells in cis but only have partial targeting specificity.

    Directory of Open Access Journals (Sweden)

    Martin Kreutz

    Full Text Available Antibody-antigen conjugates, which promote antigen-presentation by dendritic cells (DC by means of targeted delivery of antigen to particular DC subsets, represent a powerful vaccination approach. To ensure immunity rather than tolerance induction the co-administration of a suitable adjuvant is paramount. However, co-administration of unlinked adjuvant cannot ensure that all cells targeted by the antibody conjugates are appropriately activated. Furthermore, antigen-presenting cells (APC that do not present the desired antigen are equally strongly activated and could prime undesired responses against self-antigens. We, therefore, were interested in exploring targeted co-delivery of antigen and adjuvant in cis in form of antibody-antigen-adjuvant conjugates for the induction of anti-tumour immunity. In this study, we report on the assembly and characterization of conjugates consisting of DEC205-specific antibody, the model antigen ovalbumin (OVA and CpG oligodeoxynucleotides (ODN. We show that such conjugates are more potent at inducing cytotoxic T lymphocyte (CTL responses than control conjugates mixed with soluble CpG. However, our study also reveals that the nucleic acid moiety of such antibody-antigen-adjuvant conjugates alters their binding and uptake and allows delivery of the antigen and the adjuvant to cells partially independently of DEC205. Nevertheless, antibody-antigen-adjuvant conjugates are superior to antibody-free antigen-adjuvant conjugates in priming CTL responses and efficiently induce anti-tumour immunity in the murine B16 pseudo-metastasis model. A better understanding of the role of the antibody moiety is required to inform future conjugate vaccination strategies for efficient induction of anti-tumour responses.

  9. Limitation of tuning the antibody-antigen reaction by changing the value of pH and its consequence for hyperthermia.

    Science.gov (United States)

    Mleczko, J; Defort, A; Kozioł, J J; Nguyen, T T; Mirończyk, A; Zapotoczny, B; Nowak-Jary, J; Gronczewska, E; Marć, M; Dudek, M R

    2016-04-01

    Distribution of the isoelectric point (pI) was calculated for the hypervariable regions of Fab fragments of the antibody molecules, which structure is annotated in the structural antibody database SabDab. The distribution is consistent with the universal for all organisms dividing the proteome into two sets of acidic and basic proteins. It shows the additional fine structure in a form of the narrow-sized peaks of pI values. This is an explanation why a small change of the environmental pH can have a strong effect on the antibody-antigen affinity. To show this, a typical enzyme-linked immunospecific assay experiment for testing the reaction of goat anti-human IgA antibodies with human IgA immunoglobulins of saliva as antigens was modified in such a way that Fe3O4magnetic nanoparticles were added to PBS buffer. The magnetic nanoparticles were remotely heated by the radio frequency magnetic field providing the local change of temperature and pH. It was observed that short times of the heating were significantly increasing the antibody-antigen binding strength while it was not the case for a longer time. The finding discussed in the study can be useful for biopharmaceuticals using antibodies, the immunoassay techniques as well as for control over the use of hyperthermia. PMID:26634446

  10. Fabrication of fiber-optic localized surface plasmon resonance sensor and its application to detect antibody-antigen reaction of interferon-gamma

    Science.gov (United States)

    Jeong, Hyeon-Ho; Erdene, Norov; Lee, Seung-Ki; Jeong, Dae-Hong; Park, Jae-Hyoung

    2011-12-01

    A fiber-optic localized surface plasmon (FO LSPR) sensor was fabricated by gold nanoparticles (Au NPs) immobilized on the end-face of an optical fiber. When Au NPs were formed on the end-face of an optical fiber by chemical reaction, Au NPs aggregation occurred and the Au NPs were immobilized in various forms such as monomers, dimers, trimers, etc. The component ratio of the Au NPs on the end-face of the fabricated FO LSPR sensor was slightly changed whenever the sensors were fabricated in the same condition. Including this phenomenon, the FO LSPR sensor was fabricated with high sensitivity by controlling the density of Au NPs. Also, the fabricated sensors were measured for the resonance intensity for the different optical systems and analyzed for the effect on sensitivity. Finally, for application as a biosensor, the sensor was used for detecting the antibody-antigen reaction of interferon-gamma.

  11. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

    KAUST Repository

    Olimpieri, Pier Paolo

    2013-06-26

    MOTIVATION: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. RESULTS: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. AVAILABILITY: http://www.biocomputing.it/proABC. CONTACT: anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  12. PK/PD analysis of a novel pH-dependent antigen-binding antibody using a dynamic antibody-antigen binding model.

    Science.gov (United States)

    Haraya, Kenta; Tachibana, Tatsuhiko; Iwayanagi, Yuki; Maeda, Atsuhiko; Ozeki, Kazuhisa; Nezu, Junichi; Ishigai, Masaki; Igawa, Tomoyuki

    2016-04-01

    Previously, we have reported novel engineered antibody with pH-dependent antigen-binding (recycling antibody), and with both pH-dependent antigen-binding and increased FcRn-binding at neutral pH (sweeping antibody). The purpose of this study is to perform PK/PD predictions to better understand the potential applications of the antibodies as therapeutics. To demonstrate the applicability of recycling and sweeping antibodies over conventional antibodies, PK/PD analyses were performed. PK/PD parameters for antibody and antigen dynamics were estimated from the results of a pharmacokinetic study in human FcRn transgenic mice. A simulation study was performed using the estimated PK/PD parameters with various target antigen profiles. In comparison to conventional antibody, recycling antibody enhanced antibody-antigen complex clearance by 3 folds, while sweeping antibody accelerated antigen clearance by 10 folds in a pharmacokinetic study. Simulation results showed that recycling and sweeping antibodies can improve dosage frequency and reduce the required dose for target antigens with various clearances, plasma concentrations or binding kinetics. Moreover, importance of the association rate constant to enhance the beneficial effect of antibodies was shown. These results support the conclusion that recycling and sweeping antibodies can be applied to various target antigens with different profiles, and expand the number of antigens that antibodies can target. PMID:26944099

  13. Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex.

    Directory of Open Access Journals (Sweden)

    Masato Kiyoshi

    Full Text Available The optimization of antibodies is a desirable goal towards the development of better therapeutic strategies. The antibody 11K2 was previously developed as a therapeutic tool for inflammatory diseases, and displays very high affinity (4.6 pM for its antigen the chemokine MCP-1 (monocyte chemo-attractant protein-1. We have employed a virtual library of mutations of 11K2 to identify antibody variants of potentially higher affinity, and to establish benchmarks in the engineering of a mature therapeutic antibody. The most promising candidates identified in the virtual screening were examined by surface plasmon resonance to validate the computational predictions, and to characterize their binding affinity and key thermodynamic properties in detail. Only mutations in the light-chain of the antibody are effective at enhancing its affinity for the antigen in vitro, suggesting that the interaction surface of the heavy-chain (dominated by the hot-spot residue Phe101 is not amenable to optimization. The single-mutation with the highest affinity is L-N31R (4.6-fold higher affinity than wild-type antibody. Importantly, all the single-mutations showing increase affinity incorporate a charged residue (Arg, Asp, or Glu. The characterization of the relevant thermodynamic parameters clarifies the energetic mechanism. Essentially, the formation of new electrostatic interactions early in the binding reaction coordinate (transition state or earlier benefits the durability of the antibody-antigen complex. The combination of in silico calculations and thermodynamic analysis is an effective strategy to improve the affinity of a matured therapeutic antibody.

  14. 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

  15. Deserved Compensation

    Institute of Scientific and Technical Information of China (English)

    LI LI

    2010-01-01

    @@ China's National People's Congress (NPC), the top legislature, recently adopted amendments to the Law on State Compensation, granting citizens greater power to obtain compensation when their rights are violated by the state.

  16. 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...

  17. 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.

  18. Losses compensation; Compensation des pertes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    One mission of RTE (Electric Power Transportation), is to watch over the losses compensation resulting from the power transport on the electric power network. Since january 2001, RTE makes good the electric losses by the purchase of energy. To choose the marketers, a consultation has been realized by RTE. This document presents the rules concerning these losses compensation. (A.L.B.)

  19. 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.

  20. 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.

  1. POSE Algorithms for Automated Docking

    Science.gov (United States)

    Heaton, Andrew F.; Howard, Richard T.

    2011-01-01

    POSE (relative position and attitude) can be computed in many different ways. Given a sensor that measures bearing to a finite number of spots corresponding to known features (such as a target) of a spacecraft, a number of different algorithms can be used to compute the POSE. NASA has sponsored the development of a flash LIDAR proximity sensor called the Vision Navigation Sensor (VNS) for use by the Orion capsule in future docking missions. This sensor generates data that can be used by a variety of algorithms to compute POSE solutions inside of 15 meters, including at the critical docking range of approximately 1-2 meters. Previously NASA participated in a DARPA program called Orbital Express that achieved the first automated docking for the American space program. During this mission a large set of high quality mated sensor data was obtained at what is essentially the docking distance. This data set is perhaps the most accurate truth data in existence for docking proximity sensors in orbit. In this paper, the flight data from Orbital Express is used to test POSE algorithms at 1.22 meters range. Two different POSE algorithms are tested for two different Fields-of-View (FOVs) and two different pixel noise levels. The results of the analysis are used to predict future performance of the POSE algorithms with VNS data.

  2. A python-based docking program utilizing a receptor bound ligand shape: PythDock.

    Science.gov (United States)

    Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

    2011-09-01

    PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

  3. 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

  4. 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.

  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. Questioning Compensation

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Transparent management and open information needed for the fund set up to compensate victims of the 2008 Sanlu milk scandal Almost three years after the Sanlu milk scandal that caused thousands of infants in China to develop urinary disease after drinking melamine

  7. Spent fuel canister docking station

    Energy Technology Data Exchange (ETDEWEB)

    Suikki, M. [Afore Oy, Turku (Finland)

    2006-01-15

    The working report for the spent fuel canister docking station presents a design for the operation and structure of the docking equipment located in the fuel handling cell for the spent fuel in the encapsulation plant. The report contains a description of the basic requirements for the docking station equipment and their implementation, the operation of the equipment, maintenance and a cost estimate. In the designing of the equipment all the problems related with the operation have been solved at the level of principle, nevertheless, detailed designing and the selection of final components have not yet been carried out. In case of defects and failures, solutions have been considered for postulated problems, and furthermore, the entire equipment was gone through by the means of systematic risk analysis (PFMEA). During the docking station designing we came across with needs to influence the structure of the actual disposal canister for spent nuclear fuel, too. Proposed changes for the structure of the steel lid fastening screw were included in the report. The report also contains a description of installation with the fuel handling cell structures. The purpose of the docking station for the fuel handling cell is to position and to seal the disposal canister for spent nuclear fuel into a penetration located on the cell floor and to provide suitable means for executing the loading of the disposal canister and the changing of atmosphere. The designed docking station consists of a docking ring, a covering hatch, a protective cone and an atmosphere-changing cap as well as the vacuum technology pertaining to the changing of atmosphere and the inert gas system. As far as the solutions are concerned, we have arrived at rather simple structures and most of the actuators of the system are situated outside of the actual fuel handling cell. When necessary, the equipment can also be used for the dismantling of a faulty disposal canister, cut from its upper end by machining. The

  8. 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...

  9. 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.

  10. Dimerization of DOCK2 is essential for DOCK2-mediated Rac activation and lymphocyte migration.

    Science.gov (United States)

    Terasawa, Masao; Uruno, Takehito; Mori, Sayako; Kukimoto-Niino, Mutsuko; Nishikimi, Akihiko; Sanematsu, Fumiyuki; Tanaka, Yoshihiko; Yokoyama, Shigeyuki; Fukui, Yoshinori

    2012-01-01

    The migratory properties of lymphocytes depend on DOCK2, an atypical Rac activator predominantly expressed in hematopoietic cells. Although DOCK2 does not contain the Dbl homology domain typically found in guanine nucleotide exchange factors (GEFs), DOCK2 mediates the GTP-GDP exchange reaction for Rac via its DOCK homology region (DHR)-2 (also known as CZH2 or Docker) domain. DOCK2 DHR-2 domain is composed of three lobes, and Rac binding site and catalytic center are generated entirely from lobes B and C. On the other hand, lobe A has been implicated in dimer formation, yet its physiological significance remains unknown. Here, we report that lobe A-mediated DOCK2 dimerization is crucial for Rac activation and lymphocyte migration. We found that unlike wild-type DOCK2, DOCK2 mutant lacking lobe A failed to restore motility and polarity when expressed in thymoma cells and primary T cells lacking endogenous expression of DOCK2. Similar results were obtained with the DOCK2 point mutant having a defect in dimerization. Deletion of lobe A from the DHR-2 domain did not affect Rac GEF activity in vitro. However, fluorescence resonance energy transfer analyses revealed that lobe A is required for DOCK2 to activate Rac effectively during cell migration. Our results thus indicate that DOCK2 dimerization is functionally important under the physiological condition where only limited amounts of DOCK2 and Rac are localized to the plasma membrane. PMID:23050005

  11. Dimerization of DOCK2 is essential for DOCK2-mediated Rac activation and lymphocyte migration.

    Directory of Open Access Journals (Sweden)

    Masao Terasawa

    Full Text Available The migratory properties of lymphocytes depend on DOCK2, an atypical Rac activator predominantly expressed in hematopoietic cells. Although DOCK2 does not contain the Dbl homology domain typically found in guanine nucleotide exchange factors (GEFs, DOCK2 mediates the GTP-GDP exchange reaction for Rac via its DOCK homology region (DHR-2 (also known as CZH2 or Docker domain. DOCK2 DHR-2 domain is composed of three lobes, and Rac binding site and catalytic center are generated entirely from lobes B and C. On the other hand, lobe A has been implicated in dimer formation, yet its physiological significance remains unknown. Here, we report that lobe A-mediated DOCK2 dimerization is crucial for Rac activation and lymphocyte migration. We found that unlike wild-type DOCK2, DOCK2 mutant lacking lobe A failed to restore motility and polarity when expressed in thymoma cells and primary T cells lacking endogenous expression of DOCK2. Similar results were obtained with the DOCK2 point mutant having a defect in dimerization. Deletion of lobe A from the DHR-2 domain did not affect Rac GEF activity in vitro. However, fluorescence resonance energy transfer analyses revealed that lobe A is required for DOCK2 to activate Rac effectively during cell migration. Our results thus indicate that DOCK2 dimerization is functionally important under the physiological condition where only limited amounts of DOCK2 and Rac are localized to the plasma membrane.

  12. 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....

  13. 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 examin...

  14. Reducing workers' compensation costs.

    Science.gov (United States)

    Killian, M J

    1994-01-01

    Employers can reduce their workers' compensation costs by encouraging internal communication and education before and after injuries occur. Comprehensive workers' compensation programs can be developed by integrating the management of employee benefits and workers' compensation claims. PMID:10133659

  15. 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.

  16. 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...

  17. 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.

  18. Laser docking sensor engineering model

    Science.gov (United States)

    Dekome, Kent; Barr, Joseph M.

    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.

  19. Vehicle routing with cross-docking

    DEFF Research Database (Denmark)

    Wen, Min; Larsen, Jesper; Clausen, Jens;

    2009-01-01

    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...... of the VRPCD is to minimize the total travel time while respecting time window constraints at the nodes and a time horizon for the whole transportation operation. In this paper, a mixed integer programming formulation for the VRPCD is proposed. A tabu search heuristic is embedded within an adaptive memory...... values) within very short computational time....

  20. 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

  1. 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...

  2. 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.

  3. Evaluation of OMV ranging and docking systems

    Science.gov (United States)

    Mcdonald, M. W.

    1985-01-01

    The Orbital Maneuvering Vehicle (OMV) will serve as a shuttle-based or permanent space station-based vehicle designed to rendezvous and soft dock with various other free-flying space vehicles for purposes of inspection, support, and retrieval. This study is concerned primarily with the eventual need for the OMV to rendezvous and dock softly with the Edwin P. Hubble Space Telescope (ST). Utilizing the available capabilities of the large microwave anechoic chamber facility at Marshall Space Flight Center for simulating docking target vehicle motions in a free-space environment, a program is being devised for benchmark testing of rendezvous and docking sensor systems proposed for use on the OMV. A testing regimen suitable for evaluating the accuracy and tracking agility in sensing range, range rate, and angle information at close ranges (0 R 30m) has been developed.

  4. 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...

  5. Triangulation methods for automated docking

    Science.gov (United States)

    Bales, John W.

    1996-01-01

    An automated docking system must have a reliable method for determining range and orientation of the passive (target) vehicle with respect to the active vehicle. This method must also provide accurate information on the rates of change of range to and orientation of the passive vehicle. The method must be accurate within required tolerances and capable of operating in real time. The method being developed at Marshall Space Flight Center employs a single TV camera, a laser illumination system and a target consisting, in its minimal configuration, of three retro-reflectors. Two of the retro-reflectors are mounted flush to the same surface, with the third retro-reflector mounted to a post fixed midway between the other two and jutting at a right angle from the surface. For redundancy, two additional retroreflectors are mounted on the surface on a line at right angles to the line containing the first two retro-reflectors, and equally spaced on either side of the post. The target vehicle will contain a large target for initial acquisition and several smaller targets for close range.

  6. 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

  7. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment.

    NARCIS (Netherlands)

    Kufareva, I.; Rueda, M.; Katritch, V.; Stevens, R.C.; Abagyan, R.; Vroling, B.; Sanders, M.P.A.

    2011-01-01

    The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule anta

  8. 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

  9. Essays in Executive Compensation

    NARCIS (Netherlands)

    D. Zhang (Dan)

    2012-01-01

    textabstractThis dissertation focuses on how executive compensation is designed and its implications for corporate finance and government regulations. Chapter 2 analyzes several proposals to restrict CEO compensation and calibrates two models of executive compensation that describe how firms would r

  10. PTools: an opensource molecular docking library

    Directory of Open Access Journals (Sweden)

    Poulain Pierre

    2009-05-01

    Full Text Available Abstract Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure. Conclusion The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.

  11. Options in Compensation

    DEFF Research Database (Denmark)

    Flor, Christian Riis; Frimor, Hans; Munk, Claus

    2014-01-01

    We derive the optimal compensation contract in a principal–agent setting in which outcome is used to provide incentives for both effort and risky investments. To motivate investment, optimal compensation entails rewards for high as well as low outcomes, and it is increasing at the mean outcome...... to motivate effort. If rewarding low outcomes is infeasible, compensation consisting of stocks and options is a near-efficient means of overcoming the manager's induced aversion to undertaking risky investments, whereas stock compensation is not. However, stock plus option compensation may induce excessively...

  12. 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

  13. 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.

  14. 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.

  15. A New Scoring Function for Molecular Docking Based on AutoDock and AutoDock Vina.

    Science.gov (United States)

    Tanchuk, Vsevolod Yu; Tanin, Volodymyr O; Vovk, Andriy I; Poda, Gennady

    2015-01-01

    Molecular docking of small molecules in the protein binding sites is the most widely used computational technique in modern structure-based drug discovery. Although accurate prediction of binding modes of small molecules can be achieved in most cases, estimation of their binding affinities remains mediocre at best. As an attempt to improve the correlation between the inhibitory constants, pKi, and scoring, we created a new, hybrid scoring function. The new function is a linear combination of the terms of the scoring functions of AutoDock and AutoDock Vina. It was trained on 2,412 protein-ligand complexes from the PDBbind database (www.pdbbind.org.cn, version 2012) and validated on a set of 313 complexes released in the 2013 version as a test set. The new function was included in a modified version of AutoDock. The hybrid scoring function showed a statistically significant improvement in both training and test sets in terms of correlation with and root mean square and mean absolute errors in prediction of pKi values. It was also tested on the CSAR 2014 Benchmark Exercise dataset (team T) and produced reasonably good results.

  16. AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.

    Science.gov (United States)

    Santos-Martins, Diogo; Forli, Stefano; Ramos, Maria João; Olson, Arthur J

    2014-08-25

    Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.

  17. 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...

  18. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.; van Dijk, M.; Bonvin, A.M.J.J.

    2010-01-01

    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  19. 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

  20. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René

    2003-01-01

    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...

  1. 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.

  2. Docking to flexible nicotinic acetylcholine receptors

    DEFF Research Database (Denmark)

    Sander, Tommy; Bruun, Anne T; Balle, Thomas

    2010-01-01

    Computational docking to nicotinic acetylcholine receptors (nAChRs) and other members of the Cys-loop receptor family is complicated by the flexibility of the so-called C-loop. As observed in the large number of published crystal structures of the acetylcholine binding protein (AChBP), a structural...

  3. 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.

  4. Cooperation, compensation and transition

    NARCIS (Netherlands)

    Ju, Y.

    2004-01-01

    Cooperation and compensation are two important and well-linked issues in economics. The central question in cooperation is how to share the joint gains among participating players. Compensation is a specific aspect of surplus sharing problems providing incentives for agents to sacrifice their own di

  5. Medical leadership compensation framework

    OpenAIRE

    Uhlíř, Tomáš

    2009-01-01

    This master thesis deals with outlining the rationale of redesigning medical leadership compensation framework within Interior Health Authority (IH). In particular, reviews IH's organizational structure, analyses job descriptions for medical leaders, recommends improvements of communication flow across the authority and designs medical leader's compensation model.

  6. Satellite Docking Simulator with Generic Contact Dynamics Capabilities

    Science.gov (United States)

    Ma, O.; Crabtree, D.; Carr, R.; Gonthier, Y.; Martin, E.; Piedboeuf, J.-C.

    2002-01-01

    Satellite docking (and capture) systems are critical for the servicing or salvage of satellites. Satellite servicing has comparatively recently become a realistic and promising space operation/mission. Satellite servicing includes several of the following operations: rendezvous; docking (capturing); inspection; towing (transporting); refueling; refurbishing (replacement of faulty or "used-up" modules/boxes); and un-docking (releasing). Because spacecraft servicing has been, until recently non-feasible or non-economical, spacecraft servicing technology has been neglected. Accordingly, spacecraft designs have featured self- contained systems without consideration for operational servicing. Consistent with this view, most spacecrafts were designed and built without docking interfaces. If, through some mishap, a spacecraft was rendered non-operational, it was simply considered expendable. Several feasibility studies are in progress on salvaging stranded satellites (which, in fact had led to this project). The task of the designer of the docking system for a salvaging task is difficult. He/she has to work with whatever it is on orbit, and this excludes any special docking interfaces, which might have made his/her task easier. As satellite servicing becomes an accepted design requirement, many future satellites will be equipped with appropriate docking interfaces. The designer of docking systems will be faced with slightly different challenges: reliable, cost-effective, docking (and re-supply) systems. Thus, the role of designers of docking systems will increase from one of a kind, ad-hoc interfaces intended for salvaging operations, to docking systems for satellites and "caretaker" spacecraft which are meant for servicing and are produced in larger numbers. As in any space system (for which full and representative ground hardware test-beds are very expensive and often impossible to develop), simulations are mandatory for the development of systems and operations for

  7. 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.

  8. 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).

  9. 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.

  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. Combined Immunodeficiency Associated with DOCK8 Mutations

    Science.gov (United States)

    Zhang, Qian; Davis, Jeremiah C.; Lamborn, Ian T.; Freeman, Alexandra F.; Jing, Huie; Favreau, Amanda J.; Matthews, Helen F.; Davis, Joie; Turner, Maria L.; Uzel, Gulbu; Holland, Steven M.; Su, Helen C.

    2010-01-01

    BACKGROUND Recurrent sinopulmonary and cutaneous viral infections with elevated serum levels of IgE are features of some variants of combined immunodeficiency. The genetic causes of these variants are unknown. METHODS We collected longitudinal clinical data on 11 patients from eight families who had recurrent sinopulmonary and cutaneous viral infections. We performed comparative genomic hybridization arrays and targeted gene sequencing. Variants with predicted loss-of-expression mutations were confirmed by means of a quantitative reverse-transcriptase –polymerase-chain-reaction assay and immunoblotting. We evaluated the number and function of lymphocytes with the use of in vitro assays and flow cytometry. RESULTS Patients had recurrent otitis media, sinusitis, and pneumonias; recurrent Staphylococcus aureus skin infections with otitis externa; recurrent, severe herpes simplex virus or herpes zoster infections; extensive and persistent infections with molluscum contagiosum; and human papillomavirus infections. Most patients had severe atopy with anaphylaxis; several had squamous-cell carcinomas, and one had T-cell lymphoma –leukemia. Elevated serum IgE levels, hypereosinophilia, low numbers of T cells and B cells, low serum IgM levels, and variable IgG antibody responses were common. Expansion in vitro of activated CD8 T cells was impaired. Novel homozygous or compound heterozygous deletions and point mutations in the gene encoding the dedicator of cytokinesis 8 protein (DOCK8) led to the absence of DOCK8 protein in lymphocytes. CONCLUSIONS Autosomal recessive DOCK8 deficiency is associated with a novel variant of combined immunodeficiency. PMID:19776401

  12. Turbulence compensation: an overview

    Science.gov (United States)

    van Eekeren, Adam W. M.; Schutte, Klamer; Dijk, Judith; Schwering, Piet B. W.; van Iersel, Miranda; Doelman, Niek J.

    2012-06-01

    In general, long range visual detection, recognition and identification are hampered by turbulence caused by atmospheric conditions. Much research has been devoted to the field of turbulence compensation. One of the main advantages of turbulence compensation is that it enables visual identification over larger distances. In many (military) scenarios this is of crucial importance. In this paper we give an overview of several software and hardware approaches to compensate for the visual artifacts caused by turbulence. These approaches are very diverse and range from the use of dedicated hardware, such as adaptive optics, to the use of software methods, such as deconvolution and lucky imaging. For each approach the pros and cons are given and it is indicated for which scenario this approach is useful. In more detail we describe the turbulence compensation methods TNO has developed in the last years and place them in the context of the different turbulence compensation approaches and TNO's turbulence compensation roadmap. Furthermore we look forward and indicate the upcoming challenges in the field of turbulence compensation.

  13. InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.

    Science.gov (United States)

    Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

    2016-07-01

    The structural modeling of protein-protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/.

  14. 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

  15. Climate change and compensation

    DEFF Research Database (Denmark)

    Jensen, Karsten Klint; Flanagan, Tine Bech

    2013-01-01

    This paper presents a case for compensation of actual harm from climate change in the poorest countries. First, it is shown that climate change threatens to reverse the fight to eradicate poverty. Secondly, it is shown how the problems raised in the literature for compensation to some extent...... are based on misconceptions and do not apply to compensation of present actual harm. Finally, two arguments are presented to the effect that, in so far as developed countries accept a major commitment to mitigate climate change, they should also accept a commitment to address or compensate actual harm from...... climate change. The first argument appeals to the principle that if it is an injustice to cause risk of incurring harm in the future, then it is also an injustice to cause a similar harm now. The second argument appeals to the principle that if there is moral reason to reduce the risk of specific harms...

  16. ACTS Rain Fade Compensation

    Science.gov (United States)

    Coney, Thom A.

    1996-01-01

    Performance status of the Adaptive Rain Fade Compensation includes: (1) The rain fade protocol is functional detecting fades, providing an additional 10 dB of margin and seamless transitions to and from coded operation; (2) The stabilization of the link margins and the optimization of rain fade decision thresholds has resulted in improved BER performance; (3) Characterization of the fade compensation algorithm is ongoing.

  17. Optimal Sales Force Compensation

    OpenAIRE

    Matthias Kräkel; Anja Schöttner

    2014-01-01

    We analyze a dynamic moral-hazard model to derive optimal sales force compensation plans without imposing any ad hoc restrictions on the class of feasible incentive contracts. We explain when the compensation plans that are most common in practice - fixed salaries, quota-based bonuses, commissions, or a combination thereof - are optimal. Fixed salaries are optimal for small revenue-cost ratios. Quota-based bonuses (commissions) should be used if the revenue-cost ratio takes intermediate (larg...

  18. Essays in Executive Compensation

    OpenAIRE

    Zhang, Dan

    2013-01-01

    This doctoral thesis is made of three empirical research papers focused on executive compensation topics. The first chapter is a solo paper, while the second and third papers are co-authored with Antonio Parbonetti. The first chapter answers to Bushman and Smith’s (2001) call for research on compensation of executives other than CEOs. Specifically, using a sample of 586 firm-year observations over the period 2000-2009, I investigate the economic determinants and effects on shareholder va...

  19. A Comparison of Candidate Seal Designs for Future Docking Systems

    Science.gov (United States)

    Dunlap, Patrick, H., Jr.; Steinetz, Bruce, M.

    2012-01-01

    NASA is developing a new docking system to support future space exploration missions to low Earth orbit, the Moon, and other destinations. A key component of this system is the seal at the main docking interface which inhibits the loss of cabin air once docking is complete. Depending on the mission, the seal must be able to dock in either a seal-on-flange or seal-on-seal configuration. Seal-on-flange mating would occur when a docking system equipped with a seal docks to a system with a flat metal flange. This would occur when a vehicle docks to a node on the International Space Station. Seal-on-seal mating would occur when two docking systems equipped with seals dock to each other. Two types of seal designs were identified for this application: Gask-O-seals and multi-piece seals. Both types of seals had a pair of seal bulbs to satisfy the redundancy requirement. A series of performance assessments and comparisons were made between the candidate seal designs indicating that they meet the requirements for leak rate and compression and adhesion loads under a range of operating conditions. Other design factors such as part count, integration into the docking system tunnel, seal-on-seal mating, and cost were also considered leading to the selection of the multi-piece seal design for the new docking system. The results of this study can be used by designers of future docking systems and other habitable volumes to select the seal design best-suited for their particular application.

  20. 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.

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

    DEFF Research Database (Denmark)

    Olsen, Lars; Pettersson, Ingrid; Hemmingsen, Lars;

    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...... between the experimentally determined MBL-inhibitor affinities and the GOLD scores. GOLD was selected for a test including a broad spectrum of inhibitors for which experimental MBL-inhibitor binding affinities are available. This study revealed that (1) for most compound classes (dicarboxylic acids...

  2. 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.

  3. Compensation committee composition and CEO compensation – Finnish evidence

    OpenAIRE

    Uusitalo, Mikael

    2012-01-01

    PURPOSE OF THE STUDY The purpose of this study is to examine the effect of compensation committee composition on the level of CEO compensation. The composition of the compensation committee is analyzed by using five variables which are: 1) the proportion of non-independent directors, 2) the proportion of long-serving directors, 3) the proportion of CEO-directors, 4) the proportion of busy directors and 5) the presence of a blockholder on the compensation committee. CEO compensation is measure...

  4. Rendezvous and docking with remote piloted vehicles

    Science.gov (United States)

    Micheal, J. D.

    1984-01-01

    The man-in-the-loop control system requirements for the Orbital Maneuvering Vehicle (OMV) are examined. Since many similarities exist between the Teleoperator Retrieval System (TRS) and the unfolding OMV concept, a review of the TRS control system baseline along with selected design trades which led to that baseline are discussed. TRS program issues relevant to the man-in-the-loop control system design include thruster size, communication delays and TV bandwidth compression, range/range rate radar, tumbling targets, shimmed docking interface, and control system definition. A TRS vs. OMV simulation comparative study is summarized, and the major issues currently facing the control system designer on OMV are discussed.

  5. Stealth Compensation Via Retirement Benefits

    OpenAIRE

    Lucian Arye Bebchuk; Fried, Jesse M.

    2004-01-01

    This paper analyzes an important form of "stealth compensation" provided to managers of public companies. We show how boards have been able to camouflage large amount of executive compensation through the use of retirement benefits and payments. Our study highlights the significant role that camouflage and stealth compensation play in the design of compensation arrangements. Our study also highlights the significance of whether information about compensation arrangements is not merely publicl...

  6. Compensation for nuclear damage

    International Nuclear Information System (INIS)

    To secure fair and efficient compensation for damage likely to be caused by the utilisation of nuclear energy, a special civil liability regime was set up by several international conventions. Three of these conventions are in force and Spain is a Contracting Party to all three. The principles established in the first instance at European level by the Paris Convention (absolute and exclusive liability of the nuclear operator, limitation of such liability, compulsory insurance...) are intended to guarantee that possible victims of a nuclear incident will obtain compensation for damage suffered. The Brussels Convention Supplementary to the Paris Convention provides for official funds to compensate victims through intervention by the Contracting Parties. Each Contracting Party should implement these Conventions at national level by appropriate legislation, which is what Spain did with its Act on Nuclear Energy of 29th April 1964, as supplemented in 1967 by the Regulations on Cover for Nuclear Hazards. (N.E.A.)

  7. 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.

  8. 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.....

  9. Evaluation of molecular docking using polynomial empirical scoring functions.

    Science.gov (United States)

    Dias, Raquel; Timmers, Luis Fernando Saraiva Macedo; Caceres, Rafael Andrade; de Azevedo, Walter Filgueira

    2008-12-01

    Molecular docking simulations are of pivotal importance for analysis of protein-ligand interactions and also an essential resource for virtual-screening initiatives. In molecular docking simulations several possible docked structures are generated, which create an ensemble of structures representing binary complexes. Therefore, it is crucial to find the best solution for the simulation. One approach to this problem is to employ empirical scoring function to identify the best docked structure. It is expected that scoring functions show a descriptive funnel-shaped energy surface without many false minima to impair the efficiency of conformational sampling. We employed this methodology against a test set with 300 docked structures. Docking simulations of these ligands against enzyme binding pocket indicated a funnel-shaped behavior of the complexation for this system. This review compares a set of recently proposed polynomial empirical scoring functions, implemented in a program called POLSCORE, with two popular scoring function programs (XSCORE and DrugScore). Overall comparison indicated that POLSCORE works better to predict the correct docked position, for the ensemble of docked structures analyzed in the present work.

  10. 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

  11. Coase Competition and Compensation

    OpenAIRE

    Hal Varian

    1994-01-01

    I show that the Pigovian solution to a simple externalities problem and a particular Coasian solution can be viewed as competitive equilibria from different initial endowments. I also describe the ``compensation mechanism,'' a mechanism that implements either the Coasian or Pigovian solution as the outcome of an economically natural bargaining game.

  12. A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina.

    Science.gov (United States)

    Tanchuk, Vsevolod Yu; Tanin, Volodymyr O; Vovk, Andriy I; Poda, Gennady

    2016-04-01

    Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has been introduced. The new hybrid scoring function is a linear combination of the two scoring function components derived from a multiple linear regression fitting procedure. The scoring function was built on a training set of 2412 protein-ligand complexes from pdbbind database (www.pdbbind.org.cn, version 2012). A test set of 313 complexes that appeared in the 2013 version was used for validation purposes. The new hybrid scoring function performed better than the original functions, both on training and test sets of protein-ligand complexes, as measured by the non-parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root-mean-square error (RMSE) between the experimental binding affinities and the docking scores. The function also gave one of the best results among more than 20 scoring functions tested on the core set of the pdbbind database. The new AutoDock hybrid scoring function will be implemented in modified version of AutoDock.

  13. Robust adaptive backstepping neural networks control for spacecraft rendezvous and docking with input saturation.

    Science.gov (United States)

    Xia, Kewei; Huo, Wei

    2016-05-01

    This paper presents a robust adaptive neural networks control strategy for spacecraft rendezvous and docking with the coupled position and attitude dynamics under input saturation. Backstepping technique is applied to design a relative attitude controller and a relative position controller, respectively. The dynamics uncertainties are approximated by radial basis function neural networks (RBFNNs). A novel switching controller consists of an adaptive neural networks controller dominating in its active region combined with an extra robust controller to avoid invalidation of the RBFNNs destroying stability of the system outside the neural active region. An auxiliary signal is introduced to compensate the input saturation with anti-windup technique, and a command filter is employed to approximate derivative of the virtual control in the backstepping procedure. Globally uniformly ultimately bounded of the relative states is proved via Lyapunov theory. Simulation example demonstrates effectiveness of the proposed control scheme.

  14. RELIABILITY OF LENTICULAR EXPANSION COMPENSATORS

    Directory of Open Access Journals (Sweden)

    Gabriel BURLACU,

    2011-11-01

    Full Text Available Axial lenticular compensators are made to take over the longitudinal heat expansion, shock , vibration and noise, made elastic connections for piping systems. In order to have a long life for installations it is necessary that all elements, including lenticular compensators, have a good reliability. This desire can be did by technology of manufactoring and assembly of compensators, the material for lenses and by maintenance.of compensator

  15. Firm performance and CEO compensation : Determinants of CEO compensation

    OpenAIRE

    Singh, Minu; Yavuz, Cigdem

    2015-01-01

    CEO compensation is a much discussed concept in the media and in the society in general. The center of the discussion is mostly around the high CEO compensations and the gaps between the compensation to the CEOs and to rest of the employees. As this is an interesting and topical concept, we hence wanted to examine how CEO compensation is determined in firms listed on the Oslo Stock Exchange. We wanted to examine if CEOs actually get their compensation for obtained firm performance, or if ther...

  16. 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.

  17. 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

  18. Compensation Consultants and CEO Pay

    NARCIS (Netherlands)

    Kabir, Rezaul; Minhat, Marizah

    2014-01-01

    The study examines the practice of employing multiple compensation consultants. Examining data of a sample of UK companies over the period 2003–2006 we find that CEOs receive higher equity-based pay when firms employ more than one compensation consultant. An increase in the number of compensation co

  19. Game Theoretic Approach to Post-Docked Satellite Control

    Science.gov (United States)

    Hiramatsu, Takashi; Fitz-Coy, Norman G.

    2007-01-01

    This paper studies the interaction between two satellites after docking. In order to maintain the docked state with uncertainty in the motion of the target vehicle, a game theoretic controller with Stackelberg strategy to minimize the interaction between the satellites is considered. The small perturbation approximation leads to LQ differential game scheme, which is validated to address the docking interactions between a service vehicle and a target vehicle. The open-loop solution are compared with Nash strategy, and it is shown that less control efforts are obtained with Stackelberg strategy.

  20. 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.

  1. Compensability index for compensation radiotherapy after treatment interruptions

    Directory of Open Access Journals (Sweden)

    Putora Paul

    2012-12-01

    Full Text Available Abstract Background The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. Methods We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. Results The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. Conclusions The compensability index calculation may serve as a decision support system based on existing and established recommendations.

  2. 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...

  3. 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.

  4. 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.

  5. Virtual Screening with AutoDock: Theory and Practice

    Science.gov (United States)

    Cosconati, Sandro; Forli, Stefano; Perryman, Alex L.; Harris, Rodney; Goodsell, David S.; Olson, Arthur J.

    2011-01-01

    Importance to the field Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. Areas covered in this review We describe virtual screening methods that are available in the AutoDock suite of programs, and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. What the reader will gain A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. Take home message Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening. PMID:21532931

  6. 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...

  7. 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...

  8. 38 CFR 3.4 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Compensation. 3.4 Section..., Compensation, and Dependency and Indemnity Compensation General § 3.4 Compensation. (a) Compensation. This term...) Disability compensation. (1) Basic entitlement for a veteran exists if the veteran is disabled as the...

  9. Variability in docking success rates due to dataset preparation.

    Science.gov (United States)

    Corbeil, Christopher R; Williams, Christopher I; Labute, Paul

    2012-06-01

    The results of cognate docking with the prepared Astex dataset provided by the organizers of the "Docking and Scoring: A Review of Docking Programs" session at the 241st ACS national meeting are presented. The MOE software with the newly developed GBVI/WSA dG scoring function is used throughout the study. For 80 % of the Astex targets, the MOE docker produces a top-scoring pose within 2 Å of the X-ray structure. For 91 % of the targets a pose within 2 Å of the X-ray structure is produced in the top 30 poses. Docking failures, defined as cases where the top scoring pose is greater than 2 Å from the experimental structure, are shown to be largely due to the absence of bound waters in the source dataset, highlighting the need to include these and other crucial information in future standardized sets. Docking success is shown to depend heavily on data preparation. A "dataset preparation" error of 0.5 kcal/mol is shown to cause fluctuations of over 20 % in docking success rates. PMID:22566074

  10. 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.

  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. The Interplay between Director Compensation and CEO Compensation

    OpenAIRE

    Dan Lin; Lu Lin

    2014-01-01

    This paper empirically examines the determinants of director compensation and CEO compensation and investigates whether director compensation has an effect on CEO compensation. Based on 713 firms (or 2,852 firm-years) between 2007 and 2010, we find that CEO tenure is related to the ability of the CEO in influencing the board’s pay determination process. However, sitting on the board does not strengthen the CEO’s power over the board during the pay negotiation process. More importantly, we...

  13. 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.

  14. 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.

  15. 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.)

  16. 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.

  17. Sales Force Motivation and Compensation

    OpenAIRE

    Anca-Mihaela TEAU

    2013-01-01

    This article illustrate how sales managers can use sales incentives and compensations to motivate their sales team. To motivate sales people effectively, sales managers must have a thorough understanding of human needs and the concepts of motivation. They must also learn how to use the various forms of sales incentives and compensation to meet their salespeople’s needs.

  18. 78 FR 28441 - Executive Compensation

    Science.gov (United States)

    2013-05-14

    ... comments on Executive Compensation on June 5, 2009 (74 FR 26989). The public notice and comment period... compensation for a given position at similar institutions.'' \\9\\ \\8\\ 74 FR at 26990 (June 5, 2009). \\9\\ Section... Corporation Act (12 U.S.C. 1452(h)(2)). \\4\\ See 74 FR at 26990 (June 5, 2009). Additionally, the proposed...

  19. An overview of turbulence compensation

    NARCIS (Netherlands)

    Schutte, K.; Eekeren, A.W.M. van; Dijk, J.; Schwering, P.B.W.; Iersel, M. van; Doelman, N.J.

    2012-01-01

    In general, long range visual detection, recognition and identification are hampered by turbulence caused by atmospheric conditions. Much research has been devoted to the field of turbulence compensation. One of the main advantages of turbulence compensation is that it enables visual identification

  20. 38 CFR 3.459 - Death compensation.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Death compensation. 3.459..., Compensation, and Dependency and Indemnity Compensation Apportionments § 3.459 Death compensation. (a) Death compensation will be apportioned if the child or children of the deceased veteran are not in the custody of...

  1. Primary-care physician compensation.

    Science.gov (United States)

    Olson, Arik

    2012-01-01

    This article reviews existing models of physician compensation and presents information about current compensation patterns for primary-care physicians in the United States. Theories of work motivation are reviewed where they have relevance to the desired outcome of satisfied, productive physicians whose skills and expertise are retained in the workforce. Healthcare reforms that purport to bring accountability for healthcare quality and value-rather than simply volume-bring opportunities to redesign primary-care physician compensation and may allow for new compensation methodologies that increase job satisfaction. Physicians are increasingly shunning the responsibility of private practice and choosing to work as employees of a larger organization, often a hospital. Employers of physicians are seeking compensation models that reward both productivity and value. PMID:22786738

  2. A non-docking intraoperative electron beam applicator system

    Energy Technology Data Exchange (ETDEWEB)

    Palta, J.R.; Suntharalingam, N. (Thomas Jefferson Univ. Hospital, Philadelphia, PA (USA))

    1989-08-01

    A non-docking intraoperative radiation therapy electron beam applicator system for a linear accelerator has been designed to minimize the mechanical, electrical, and tumor visualization problems associated with a docking system. A number of technical innovations have been used in the design of this system. These include: (a) a new intraoperative radiation therapy cone design that gives a better dose uniformity in the treatment volume at all depths; (b) a collimation system which reduces the leakage radiation dose to tissues outside the intraoperative radiation therapy cone; (c) a non-docking system with a translational accuracy of 2 mm and a rotational accuracy of 0.5 degrees; and (d) a rigid clamping system for the cones. A comprehensive set of dosimetric characteristics of the intraoperative radiation therapy applicator system is presented.

  3. Molecular docking and structure-based drug design strategies.

    Science.gov (United States)

    Ferreira, Leonardo G; Dos Santos, Ricardo N; Oliva, Glaucius; Andricopulo, Adriano D

    2015-07-22

    Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  4. 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.

  5. SYNTHESIS, DOCKING AND BIOLOGICAL STUDIES OF THE LINEAR TETRAPEPTIDE PWPV

    Directory of Open Access Journals (Sweden)

    M. Himaja

    2012-06-01

    Full Text Available Linear Tetrapeptides L-PWPV (Pro-Trp-Pro-Val was designed and synthesized by solution phase peptide synthesis based on dock score. The molecular docking studies of the designed tetrapeptide L-PWPV was carried out using Molegro Virtual Docker software for tumor cancer protein(1OLG. The linear tetrapeptide was synthesized by coupling protected amino acids (dipeptides using EDC (ethyl-3-(N,N-dimethylaminopropyl carbodiimide as coupling reagent. The compounds were analyzed by FTIR, 1H NMR and MASS data and subjected to antioxidant activity using 1,1-dipheny-2-picryl-hydrazil (DPPH method and insecticidal activity using Morita et al method.

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

    DEFF Research Database (Denmark)

    Petersen, Hanne Løhmann; Røpke, Stefan

    2011-01-01

    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......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...

  7. 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.

  8. Compensated pulsed alternator

    International Nuclear Information System (INIS)

    This invention relates to an electromechanical energy converter with inertial energy storage. The device, a single phase, two or multi-pole alternator with stationary field coils, and a rotating armature is provided. The rotor itself may be of laminated steel for slower pulses or for faster pulses should be nonmagnetic and electrically nonconductive in order to allow rapid penetration of the field as the armature coil rotates. The armature coil comprises a plurality of power generating conductors mounted on the rotor. The alternator may also include a stationary or counterrotating compensating coil to increase the output voltage thereof and to reduce the internal impedance of the alternator at the moment of peak output. As the machine voltage rises sinusoidally, an external trigger switch is adapted to be closed at the appropriate time to create the desired output current from said alternator to an external load circuit, and as the output current passes through zero a self-commutating effect is provided to allow the switch to disconnect the generator from the external circuit

  9. 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.

  10. An overview of turbulence compensation

    Science.gov (United States)

    Schutte, Klamer; van Eekeren, Adam W. M.; Dijk, Judith; Schwering, Piet B. W.; van Iersel, Miranda; Doelman, Niek J.

    2012-09-01

    In general, long range visual detection, recognition and identification are hampered by turbulence caused by atmospheric conditions. Much research has been devoted to the field of turbulence compensation. One of the main advantages of turbulence compensation is that it enables visual identification over larger distances. In many (military) scenarios this is of crucial importance. In this paper we give an overview of several software and hardware approaches to compensate for the visual artifacts caused by turbulence. These approaches are very diverse and range from the use of dedicated hardware, such as adaptive optics, to the use of software methods, such as deconvolution and lucky imaging. For each approach the pros and cons are given and it is indicated for which type of scenario this approach is useful. In more detail we describe the turbulence compensation methods TNO has developed in the last years and place them in the context of the different turbulence compensation approaches and TNO's turbulence compensation roadmap. Furthermore we look forward and indicate the upcoming challenges in the field of turbulence compensation.

  11. 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

  12. 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...

  13. A fast flexible docking method using an incremental construction algorithm.

    Science.gov (United States)

    Rarey, M; Kramer, B; Lengauer, T; Klebe, G

    1996-08-23

    We present an automatic method for docking organic ligands into protein binding sites. The method can be used in the design process of specific protein ligands. It combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand. If the ligand is flexible, it can adopt a large variety of different conformations. Each such minimum in conformational space presents a potential candidate for the conformation of the ligand in the complexed state. Our docking method samples the conformation space of the ligand on the basis of a discrete model and uses a tree-search technique for placing the ligand incrementally into the active site. For placing the first fragment of the ligand into the protein, we use hashing techniques adapted from computer vision. The incremental construction algorithm is based on a greedy strategy combined with efficient methods for overlap detection and for the search of new interactions. We present results on 19 complexes of which the binding geometry has been crystallographically determined. All considered ligands are docked in at most three minutes on a current workstation. The experimentally observed binding mode of the ligand is reproduced with 0.5 to 1.2 A rms deviation. It is almost always found among the highest-ranking conformations computed.

  14. Application of the docking program SOL for CSAR benchmark.

    Science.gov (United States)

    Sulimov, Alexey V; Kutov, Danil C; Oferkin, Igor V; Katkova, Ekaterina V; Sulimov, Vladimir B

    2013-08-26

    This paper is devoted to results obtained by the docking program SOL and the post-processing program DISCORE at the CSAR benchmark. SOL and DISCORE programs are described. SOL is the original docking program developed on the basis of the genetic algorithm, MMFF94 force field, rigid protein, precalculated energy grid including desolvation in the frame of simplified GB model, vdW, and electrostatic interactions and taking into account the ligand internal strain energy. An important SOL feature is the single- or multi-processor performance for up to hundreds of CPUs. DISCORE improves the binding energy scoring by the local energy optimization of the ligand docked pose and a simple linear regression on the base of available experimental data. The docking program SOL has demonstrated a good ability for correct ligand positioning in the active sites of the tested proteins in most cases of CSAR exercises. SOL and DISCORE have not demonstrated very exciting results on the protein-ligand binding free energy estimation. Nevertheless, for some target proteins, SOL and DISCORE were among the first in prediction of inhibition activity. Ways to improve SOL and DISCORE are discussed.

  15. 18 CFR 1304.204 - Docks, piers, and boathouses.

    Science.gov (United States)

    2010-04-01

    ... structure of the maximum size, TVA shall determine the size of facility that may be approved. Applicants are... responsible for submitting plans for proposed docks, piers, and boathouses that conform to the size standards... structure. Access walkways to the water-use structure are not included in calculating the 1000-foot area....

  16. 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.

  17. Dissecting Nck/Dock Signaling Pathways in Drosophila Visual System

    Directory of Open Access Journals (Sweden)

    2005-04-01

    Full Text Available The establishment of neuronal connections during embryonic development requires the precise guidance and targeting of the neuronal growth cone, an expanded cellular structure at the leading tip of a growing axon. The growth cone contains sophisticated signaling systems that allow the rapid communication between guidance receptors and the actin cytoskeleton in generating directed motility. Previous studies demonstrated a specific role for the Nck/Dock SH2/SH3 adapter protein in photoreceptor (R cell axon guidance and target recognition in the Drosophila visual system, suggesting strongly that Nck/Dock is one of the long-sought missing links between cell surface receptors and the actin cytoskeleton. In this review, I discuss the recent progress on dissecting the Nck/Dock signaling pathways in R-cell growth cones. These studies have identified additional key components of the Nck/Dock signaling pathways for linking the receptor signaling to the remodeling of the actin cytoskeleton in controlling growth-cone motility.

  18. I-AUV Docking and Panel Intervention at Sea

    Directory of Open Access Journals (Sweden)

    Narcís Palomeras

    2016-10-01

    Full Text Available The use of commercially available autonomous underwater vehicles (AUVs has increased during the last fifteen years. While they are mainly used for routine survey missions, there is a set of applications that nowadays can be only addressed by manned submersibles or work-class remotely operated vehicles (ROVs equipped with teleoperated arms: the intervention applications. To allow these heavy vehicles controlled by human operators to perform intervention tasks, underwater structures like observatory facilities, subsea panels or oil-well Christmas trees have been adapted, making them more robust and easier to operate. The TRITON Spanish founded project proposes the use of a light-weight intervention AUV (I-AUV to carry out intervention applications simplifying the adaptation of these underwater structures and drastically reducing the operational cost. To prove this concept, the Girona 500 I-AUV is used to autonomously dock into an adapted subsea panel and once docked perform an intervention composed of turning a valve and plugging in/unplugging a connector. The techniques used for the autonomous docking and manipulation as well as the design of an adapted subsea panel with a funnel-based docking system are presented in this article together with the results achieved in a water tank and at sea.

  19. Fundamentals of compensation and benefits.

    Science.gov (United States)

    Diorio, J A; Fallon, L F

    2001-01-01

    The authors discuss the objectives of compensation programs--including direct and indirect forms of reward--and employee motivation. Job descriptions and job evaluations are also explored. PMID:11401793

  20. CEO Compensation and Bank Performance

    OpenAIRE

    Athar, Iqbal; Khan, Muhammad Irfan; Ali, Saffar

    2012-01-01

    This study sets out to discover the determinants of compensation of the chief executive officers in the banking industry of Pakistan. Accounting based performance measures and size of the firm have been used as predictors. Results of the study are consistent with arguments, suggesting significant and positive impact of size (assets) of the firm on CEO compensation while no association is found with either of the performance measure of the firm except income before tax (IBT). Return on Assets ...

  1. Recent trends in compensation practices

    OpenAIRE

    David E. Lebow; Louise Sheiner; Lawrence Slifman; Martha Starr-McCluer

    1999-01-01

    According to some accounts, compensation practices have recently been undergoing marked changes, with an increasing number of firms said to be substituting lump-sum payments for regular pay increases, allowing for greater variability of remuneration across individuals or groups, and making greater use of profit sharing or stock options. Many of these practices are outside the scope of the typical measures of economy-wide compensation growth. Moreover, intensified use of these schemes ought to...

  2. Option compensation and industry competition

    OpenAIRE

    Wong, KP; Stoughton, NM

    2009-01-01

    Compensation policy has become one of the most important ingredients of corporate governance. In this paper we take a new look at the issue, by contrasting the use of options with that of stock. We do this by integrating the repricing or resetting aspect of options with that of industrial structure. We show that industry competition may play an important role in dictating which form of compensation is optimal. When aggressive competition for key professional staff is an issue, the flexibility...

  3. BOARD STRUCTURE AND CEO COMPENSATION

    OpenAIRE

    Anjam, Zeshan

    2010-01-01

    This study examines the relationship between board structure (non executive directors, executive directors and independent non executive directors) and CEO compensation, in the context of an emerging and developing economy of Pakistan in year 2009. Most of the previous studies about board structure and CEO compensation are based in developed economies but this study is about a developing and emerging economy Pakistan and possibly this attempt will contributes to literature. Data for 86 listed...

  4. Compensation: current thinking in France

    International Nuclear Information System (INIS)

    Nuclear third party Liability law constitutes an exception to the general law of tort liability in several respects, notably the channelling of all liability to the nuclear operator even where the operator has not been at fault, and the obligation imposed upon the operator to provide financial security covering its liability. In addition, French law gives priority to compensating personal injuries, fixes the list of radioactively-induced diseases and establishes compensation based on a lump sum payment. The Group examined how these principles could be concretely implemented. It recommended two actions be taken before all else and as soon as possible: the creation of a medical group responsible for ongoing health surveillance apart from any possibility of an accident; and the establishment of a standard compensation agreement which would be prepared in advance and in consultation with interested stakeholders, to allow for compensation to be distributed quickly. Concerning organisational matters, the Group proposed setting up a 'Monitoring Committee' which would bring together all interested parties. The Group also investigated the possibility of setting up a 'One-Stop Shop' which would enable victims to contact one single agency in their quest for compensation for damage suffered, regardless of the source of the compensation funds. (author)

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

    Directory of Open Access Journals (Sweden)

    Katelyn E Mills

    Full Text Available 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.

  6. 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

  7. 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

  8. 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.

  9. Safety in earth orbit study. Volume 2: Analysis of hazardous payloads, docking, on-board survivability

    Science.gov (United States)

    1972-01-01

    Detailed and supporting analyses are presented of the hazardous payloads, docking, and on-board survivability aspects connected with earth orbital operations of the space shuttle program. The hazards resulting from delivery, deployment, and retrieval of hazardous payloads, and from handling and transport of cargo between orbiter, sortie modules, and space station are identified and analyzed. The safety aspects of shuttle orbiter to modular space station docking includes docking for assembly of space station, normal resupply docking, and emergency docking. Personnel traffic patterns, escape routes, and on-board survivability are analyzed for orbiter with crew and passenger, sortie modules, and modular space station, under normal, emergency, and EVA and IVA operations.

  10. 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

  11. 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

  12. 29 CFR 525.6 - Compensable time.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Compensable time. 525.6 Section 525.6 Labor Regulations... WITH DISABILITIES UNDER SPECIAL CERTIFICATES § 525.6 Compensable time. Individuals employed subject to this part must be compensated for all hours worked. Compensable time includes not only those...

  13. 14 CFR 158.53 - Collection compensation.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Collection compensation. 158.53 Section 158... Collection compensation. (a) As compensation for collecting, handling, and remitting the PFC revenue, the... a new compensation level based on an analysis of the data provided under paragraph (c)(1) of...

  14. 48 CFR 752.7007 - Personnel compensation.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Personnel compensation... Personnel compensation. The following clause shall be used in all USAID cost-reimbursement contracts. Personnel Compensation (JUL 2007) (a) Direct compensation of the Contractor's personnel will be...

  15. 44 CFR 295.21 - Allowable compensation.

    Science.gov (United States)

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Allowable compensation. 295... OF HOMELAND SECURITY CERRO GRANDE FIRE ASSISTANCE CERRO GRANDE FIRE ASSISTANCE Compensation Available Under the CGFAA § 295.21 Allowable compensation. (a) Allowable compensation. The CGFAA provides for...

  16. 22 CFR 96.34 - Compensation.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Compensation. 96.34 Section 96.34 Foreign... Financial and Risk Management § 96.34 Compensation. (a) The agency or person does not compensate any... for compensation within the intercountry adoption community in that country, to the extent that...

  17. 30 CFR 90.103 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Compensation. 90.103 Section 90.103 Mineral..., Rights of Part 90 Miners § 90.103 Compensation. (a) The operator shall compensate each Part 90 miner at... part. (d) In addition to the compensation required to be paid under paragraphs (a), (b) and (c) of...

  18. 48 CFR 970.2270 - Unemployment compensation.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Unemployment compensation... Unemployment compensation. (a) Each state has its own unemployment compensation system to provide payments to... unemployment compensation benefits through a payroll tax on employers. Most DOE contractors are subject to...

  19. 43 CFR 4.355 - Omitted compensation.

    Science.gov (United States)

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Omitted compensation. 4.355 Section 4.355... Compensation § 4.355 Omitted compensation. When, subsequent to the issuance of a final order determining heirs under § 4.352, it is found that certain additional compensation had been due the decedent and had...

  20. 12 CFR 620.31 - Compensation committees.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Compensation committees. 620.31 Section 620.31... Association Audit and Compensation Committees § 620.31 Compensation committees. Each Farm Credit bank and association must establish and maintain a compensation committee by adopting a written charter describing...

  1. 7 CFR 930.133 - Compensation rate.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Compensation rate. 930.133 Section 930.133 Agriculture... Regulations § 930.133 Compensation rate. A compensation rate of $250 per meeting shall be paid to the public member and to the alternate public member when attending Board meetings. Such compensation is a...

  2. 12 CFR 9.15 - Fiduciary compensation.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Fiduciary compensation. 9.15 Section 9.15 Banks... BANKS Regulations § 9.15 Fiduciary compensation. (a) Compensation of bank. If the amount of a national bank's compensation for acting in a fiduciary capacity is not set or governed by applicable law,...

  3. 23 CFR 751.15 - Just compensation.

    Science.gov (United States)

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Just compensation. 751.15 Section 751.15 Highways... AND ACQUISITION § 751.15 Just compensation. (a) Just compensation shall be paid the owner for the... removed, relocated, or disposed of pursuant to 23 U.S.C. 136. (b) No rights to compensation accrue until...

  4. 12 CFR 7.2011 - Compensation plans.

    Science.gov (United States)

    2010-01-01

    ... Corporate Practices § 7.2011 Compensation plans. Consistent with safe and sound banking practices and the compensation provisions of 12 CFR part 30, a national bank may adopt compensation plans, including, among... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Compensation plans. 7.2011 Section 7.2011...

  5. X-Chromosome dosage compensation.

    Science.gov (United States)

    Meyer, Barbara J

    2005-01-01

    In mammals, flies, and worms, sex is determined by distinctive regulatory mechanisms that cause males (XO or XY) and females (XX) to differ in their dose of X chromosomes. In each species, an essential X chromosome-wide process called dosage compensation ensures that somatic cells of either sex express equal levels of X-linked gene products. The strategies used to achieve dosage compensation are diverse, but in all cases, specialized complexes are targeted specifically to the X chromosome(s) of only one sex to regulate transcript levels. In C. elegans, this sex-specific targeting of the dosage compensation complex (DCC) is controlled by the same developmental signal that establishes sex, the ratio of X chromosomes to sets of autosomes (X:A signal). Molecular components of this chromosome counting process have been defined. Following a common step of regulation, sex determination and dosage compensation are controlled by distinct genetic pathways. C. elegans dosage compensation is implemented by a protein complex that binds both X chromosomes of hermaphrodites to reduce transcript levels by one-half. The dosage compensation complex resembles the conserved 13S condensin complex required for both mitotic and meiotic chromosome resolution and condensation, implying the recruitment of ancient proteins to the new task of regulating gene expression. Within each C. elegans somatic cell, one of the DCC components also participates in the separate mitotic/meiotic condensin complex. Other DCC components play pivotal roles in regulating the number and distribution of crossovers during meiosis. The strategy by which C. elegans X chromosomes attract the condensin-like DCC is known. Small, well-dispersed X-recognition elements act as entry sites to recruit the dosage compensation complex and to nucleate spreading of the complex to X regions that lack recruitment sites. In this manner, a repressed chromatin state is spread in cis over short or long distances, thus establishing the

  6. ATTRACT and PTools: open source programs for protein-protein docking.

    Science.gov (United States)

    Schneider, Sebastian; Saladin, Adrien; Fiorucci, Sébastien; Prévost, Chantal; Zacharias, Martin

    2012-01-01

    The prediction of the structure of protein-protein complexes based on structures or structural models of isolated partners is of increasing importance for structural biology and bioinformatics. The ATTRACT program can be used to perform systematic docking searches based on docking energy minimization. It is part of the object-oriented PTools library written in Python and C++. The library contains various routines to manipulate protein structures, to prepare and perform docking searches as well as analyzing docking results. It also intended to facilitate further methodological developments in the area of macromolecular docking that can be easily integrated. Here, we describe the application of PTools to perform systematic docking searches and to analyze the results. In addition, the possibility to perform multi-component docking will also be presented.

  7. 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

  8. Correlation Techniques as Applied to Pose Estimation in Space Station Docking

    Science.gov (United States)

    Rollins, J. Michael; Juday, Richard D.; Monroe, Stanley E., Jr.

    2002-01-01

    The telerobotic assembly of space-station components has become the method of choice for the International Space Station (ISS) because it offers a safe alternative to the more hazardous option of space walks. The disadvantage of telerobotic assembly is that it does not provide for direct arbitrary views of mating interfaces for the teleoperator. Unless cameras are present very close to the interface positions, such views must be generated graphically, based on calculated pose relationships derived from images. To assist in this photogrammetric pose estimation, circular targets, or spots, of high contrast have been affixed on each connecting module at carefully surveyed positions. The appearance of a subset of spots essentially must form a constellation of specific relative positions in the incoming digital image stream in order for the docking to proceed. Spot positions are expressed in terms of their apparent centroids in an image. The precision of centroid estimation is required to be as fine as 1I20th pixel, in some cases. This paper presents an approach to spot centroid estimation using cross correlation between spot images and synthetic spot models of precise centration. Techniques for obtaining sub-pixel accuracy and for shadow, obscuration and lighting irregularity compensation are discussed.

  9. 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

  10. 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

  11. 75 FR 49595 - Performance of Functions; Claims for Compensation Under the Federal Employees' Compensation Act...

    Science.gov (United States)

    2010-08-13

    ... Labor Office of Workers' Compensation Programs 20 CFR Parts 1, 10, and 25 Performance of Functions; Claims for Compensation Under the Federal Employees' Compensation Act; Compensation for Disability and... Workers' Compensation Programs 20 CFR Parts 1, 10, and 25 RIN 1240-AA03 Performance of Functions;...

  12. Host state incentives and compensation:

    International Nuclear Information System (INIS)

    After reviewing several options for selecting a host state, the Commission elected to proceed with anoption that builds upon developing grass-roots acceptance and support. To foster such support the Commission has adopted an incentives and compensation package. The purpose of the package is that the incentives and compensations offered are designed to encourage an objective and unbiased review of accepting the responsibilities of a host state or community, and the package helps to guarantee that a facility will become a state/community asset and not impose economic, environmenta, or social hardships for the host community. This report, which describes the Commission's host state incentive and compensation package, the monetary benefit to the host community and state will be substantial. Community benefits will exceed $40 million over 20 years and benefits to the state will be approximately $24 million over the 20-year expected life of the facility. 10 refs., 4 tabs

  13. Compensation for electrical converter nonlinearities

    Science.gov (United States)

    Perisic, Milun; Ransom, Ray M; Kajouke, Lateef A

    2013-11-19

    Systems and methods are provided for delivering energy from an input interface to an output interface. An electrical system includes an input interface, an output interface, an energy conversion module between the input interface and the output interface, an inductive element between the input interface and the energy conversion module, and a control module. The control module determines a compensated duty cycle control value for operating the energy conversion module to produce a desired voltage at the output interface and operates the energy conversion module to deliver energy to the output interface with a duty cycle that is influenced by the compensated duty cycle control value. The compensated duty cycle control value is influenced by the current through the inductive element and accounts for voltage across the switching elements of the energy conversion module.

  14. 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。

  15. Docking Studies of Phthalimide Pharmacophore as a Sodium Channel Blocker

    Directory of Open Access Journals (Sweden)

    Maryam Iman

    2013-09-01

    Full Text Available   Objective(s: Recently, phthalimide derivatives were designed based on ameltolide and thalidomide as they possess a similar degree of anticonvulsant potency due to their phenytoin-like profile. The ability of phthalimide pharmacophore to interact with neuronal voltage-dependent sodium channels was studied in the batrachotoxin affinity assay. Therefore, in the present study, a series of 19 compounds of phthalimide pharmacophore possessing a variety of substituents (NO2, NH2 , Me, Cl, COOH, MeO at 2-, 3-, and 4- position of the N-phenyl ring and N-(3-amino-2-methylphenyl succinimide, were subjected to docking studies in order to inhibit voltage-gated sodium channels.   Materials and Methods : Chemical structures of all compounds were designed using HYPERCHEM program and Conformational studies were performed through semi-empirical molecular orbital calculations method followed by PM3 force field. Total energy gradient calculated as a root mean square (RMS value, until the RMS gradient was 0.01 kcal mol-1. Among all energy minima conformers, the global minimum of compounds was used in docking calculations. Using a model of the open pore of Na channels, docking study was performed by AUTODOCK4.2 program. Results : Docking studies have revealed that these types of ligands interacted mainly with II-S6 residues of NaV1.2 through making hydrogen bonds and have additional hydrophobic interactions with domain I, II, III and IV in the channel's inner pore. Conclusion   : These computational studies have displayed that these compounds are capable of inhibiting Na channel, efficiently.

  16. Electronic amplifiers for automatic compensators

    CERN Document Server

    Polonnikov, D Ye

    1965-01-01

    Electronic Amplifiers for Automatic Compensators presents the design and operation of electronic amplifiers for use in automatic control and measuring systems. This book is composed of eight chapters that consider the problems of constructing input and output circuits of amplifiers, suppression of interference and ensuring high sensitivity.This work begins with a survey of the operating principles of electronic amplifiers in automatic compensator systems. The succeeding chapters deal with circuit selection and the calculation and determination of the principal characteristics of amplifiers, as

  17. Adaptive Motion Compensation in Radiotherapy

    CERN Document Server

    Murphy, Martin J

    2011-01-01

    External-beam radiotherapy has long been challenged by the simple fact that patients can (and do) move during the delivery of radiation. Recent advances in imaging and beam delivery technologies have made the solution--adapting delivery to natural movement--a practical reality. Adaptive Motion Compensation in Radiotherapy provides the first detailed treatment of online interventional techniques for motion compensation radiotherapy. This authoritative book discusses: Each of the contributing elements of a motion-adaptive system, including target detection and tracking, beam adaptation, and pati

  18. Depth Compensated Spectral Domain Optical Coherence Tomography via Digital Compensation

    CERN Document Server

    Boroomand, Ameneh; Shafiee, Mohammad Javad; Bizheva, Kostadinka; Wong, Alexander

    2015-01-01

    Spectral Domain Optical Coherence Tomography (SD-OCT) is a well-known imaging modality which allows for \\textit{in-vivo} visualization of the morphology of different biological tissues at cellular level resolutions. The overall SD-OCT imaging quality in terms of axial resolution and Signal-to-Noise Ratio (SNR) degrades with imaging depth, while the lateral resolution degrades with distance from the focal plane. This image quality degradation is due both to the design of the SD-OCT imaging system and the optical properties of the imaged object. Here, we present a novel Depth Compensated SD-OCT (DC-OCT) system that integrates a Depth Compensating Digital Signal Processing (DC-DSP) module to improve the overall imaging quality via digital compensation. The designed DC-DSP module can be integrated to any SD-OCT system and is able to simultaneously compensate for the depth-dependent loss of axial and lateral resolutions, depth-varying SNR, as well as sidelobe artifact for improved imaging quality. The integrated D...

  19. Fragility of Floating Docks for Small Craft Marinas

    Science.gov (United States)

    Keen, A.; Eskijian, M.; Lynett, P. J.; Ayca, A.

    2015-12-01

    Because of the damage resulting from the 2010 Chile and 2011 Japanese tele-tsunamis, damage to the small craft marinas in California has become an important concern. This paper will explain the methodology and results used to simulate the demand and also the structural capacity of the floating dock system, composed of floating docks, fingers and moored vessels during tsunami events. The intent is to develop a predictive tool to understand the vulnerability of California's small craft harbors to tsunami events. To validate the methodology, the probabilistic model will be applied to Santa Cruz Harbor. Maps of maximum velocity and mean current direction from the 2011 Japan tsunami have been developed using a numerical model. Cleat and pile guide locations will be recorded and georeferenced from aerial images before the event. The fragility curves for each dock/finger system will be compared with damage reports and aerial images from just after the tsunami event. A discussion of how the fragility curves compare with the damage reports will be included. It is anticipated that these curves will be useful to marina operators to use as a tool to determine where rehabilitation might be necessary to mitigate some of the damage from the next event. Conclusions will focus on how results can be used by marina operators to reduce harbor vulnerability to tsunamis.

  20. Ultrafast de novo docking combining pharmacophores and combinatorics.

    Science.gov (United States)

    Gastreich, Marcus; Lilienthal, Markus; Briem, Hans; Claussen, Holger

    2006-12-01

    We report on a successful de novo design approach which relies on the combination of multi-million compound combinatorial docking under receptor-based pharmacophore constraints. Inspired by a rationale by A.R. Leach et al., we document on the unification of two steps into one for ligand assembly. In the original work, fragments known to bind in protein active sites were connected forming novel ligand compounds by means of generic skeleton linkers and following a combinatorial approach. In our approach, the knowledge of fragments binding to the protein has been expressed in terms of a receptor-based pharmacophore definition. The combinatorial linking step is performed in situ during docking, starting from combinatorial libraries. Three sample scenarios growing in size and complexity (combinatorial libraries of 1 million, 1.3 million, and 22.4 million compounds) have been created to illustrate the method. Docking could be accomplished between minutes and several hours depending on the outset; the results were throughout promising. Technically, a module compatibility between FlexX(C) and FlexX-Pharm has been established. The background is explained, and the crucial points from an information scientist's perspective are highlighted.

  1. Molecular Docking and Structure-Based Drug Design Strategies

    Directory of Open Access Journals (Sweden)

    Leonardo G. Ferreira

    2015-07-01

    Full Text Available Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  2. In Silico Docking of HNF-1a Receptor Ligands

    Directory of Open Access Journals (Sweden)

    Gumpeny Ramachandra Sridhar

    2012-01-01

    Full Text Available Background. HNF-1a is a transcription factor that regulates glucose metabolism by expression in various tissues. Aim. To dock potential ligands of HNF-1a using docking software in silico. Methods. We performed in silico studies using HNF-1a protein 2GYP·pdb and the following softwares: ISIS/Draw 2.5SP4, ARGUSLAB 4.0.1, and HEX5.1. Observations. The docking distances (in angstrom units: 1 angstrom unit (Å = 0.1 nanometer or  metres with ligands in decreasing order are as follows: resveratrol (3.8 Å, aspirin (4.5 Å, stearic acid (4.9 Å, retinol (6.0 Å, nitrazepam (6.8 Å, ibuprofen (7.9 Å, azulfidine (9.0 Å, simvastatin (9.0 Å, elaidic acid (10.1 Å, and oleic acid (11.6 Å. Conclusion. HNF-1a domain interacted most closely with resveratrol and aspirin

  3. Regulation of synaptic vesicle docking by different classes of macromolecules in active zone material.

    Directory of Open Access Journals (Sweden)

    Joseph A Szule

    Full Text Available The docking of synaptic vesicles at active zones on the presynaptic plasma membrane of axon terminals is essential for their fusion with the membrane and exocytosis of their neurotransmitter to mediate synaptic impulse transmission. Dense networks of macromolecules, called active zone material, (AZM are attached to the presynaptic membrane next to docked vesicles. Electron tomography has shown that some AZM macromolecules are connected to docked vesicles, leading to the suggestion that AZM is somehow involved in the docking process. We used electron tomography on the simply arranged active zones at frog neuromuscular junctions to characterize the connections of AZM to docked synaptic vesicles and to search for the establishment of such connections during vesicle docking. We show that each docked vesicle is connected to 10-15 AZM macromolecules, which fall into four classes based on several criteria including their position relative to the presynaptic membrane. In activated axon terminals fixed during replacement of docked vesicles by previously undocked vesicles, undocked vesicles near vacated docking sites on the presynaptic membrane have connections to the same classes of AZM macromolecules that are connected to docked vesicles in resting terminals. The number of classes and the total number of macromolecules to which the undocked vesicles are connected are inversely proportional to the vesicles' distance from the presynaptic membrane. We conclude that vesicle movement toward and maintenance at docking sites on the presynaptic membrane are directed by an orderly succession of stable interactions between the vesicles and distinct classes of AZM macromolecules positioned at different distances from the membrane. Establishing the number, arrangement and sequence of association of AZM macromolecules involved in vesicle docking provides an anatomical basis for testing and extending concepts of docking mechanisms provided by biochemistry.

  4. 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.

  5. Docking validation resources: protein family and ligand flexibility experiments.

    Science.gov (United States)

    Mukherjee, Sudipto; Balius, Trent E; Rizzo, Robert C

    2010-11-22

    A database consisting of 780 ligand-receptor complexes, termed SB2010, has been derived from the Protein Databank to evaluate the accuracy of docking protocols for regenerating bound ligand conformations. The goal is to provide easily accessible community resources for development of improved procedures to aid virtual screening for ligands with a wide range of flexibilities. Three core experiments using the program DOCK, which employ rigid (RGD), fixed anchor (FAD), and flexible (FLX) protocols, were used to gauge performance by several different metrics: (1) global results, (2) ligand flexibility, (3) protein family, and (4) cross-docking. Global spectrum plots of successes and failures vs rmsd reveal well-defined inflection regions, which suggest the commonly used 2 Å criteria is a reasonable choice for defining success. Across all 780 systems, success tracks with the relative difficulty of the calculations: RGD (82.3%) > FAD (78.1%) > FLX (63.8%). In general, failures due to scoring strongly outweigh those due to sampling. Subsets of SB2010 grouped by ligand flexibility (7-or-less, 8-to-15, and 15-plus rotatable bonds) reveal that success degrades linearly for FAD and FLX protocols, in contrast to RGD, which remains constant. Despite the challenges associated with FLX anchor orientation and on-the-fly flexible growth, success rates for the 7-or-less (74.5%) and, in particular, the 8-to-15 (55.2%) subset are encouraging. Poorer results for the very flexible 15-plus set (39.3%) indicate substantial room for improvement. Family-based success appears largely independent of ligand flexibility, suggesting a strong dependence on the binding site environment. For example, zinc-containing proteins are generally problematic, despite moderately flexible ligands. Finally, representative cross-docking examples, for carbonic anhydrase, thermolysin, and neuraminidase families, show the utility of family-based analysis for rapid identification of particularly good or bad

  6. Can Education Compensate for Society?

    Science.gov (United States)

    Pring, Richard

    2011-01-01

    The extent to which education can compensate for social disadvantage is a matter of political controversy, especially in the context of policies for social mobility. On the one hand, to blame poor achievement on social class or poverty was seen to dodge the professional responsibility of teachers. On the other, the strong correlation between…

  7. Ongoing transients in carbonate compensation

    NARCIS (Netherlands)

    Boudreau, B.P.; Middelburg, J.J.; Hofmann, A.F.; Meysman, F.J.R.

    2010-01-01

    Uptake of anthropogenic CO2 is acidifying the oceans. Over the next 2000 years, this will modify the dissolution and preservation of sedimentary carbonate. By coupling new formulas for the positions of the calcite saturation horizon, zsat, the compensation depth, zcc, and the snowline, zsnow, to a b

  8. Compensation for oil pollution damage

    Science.gov (United States)

    Matugina, E. G.; Glyzina, T. S.; Kolbysheva, Yu V.; Klyuchnikov, A. S.; Vusovich, O. V.

    2015-11-01

    The commitment of national industries to traditional energy sources, as well as constantly growing energy demand combined with adverse environmental impact of petroleum production and transportation urge to establish and maintain an appropriate legal and administrative framework for oil pollution damage compensation. The article considers management strategies for petroleum companies that embrace not only production benefits but also environmental issues.

  9. Working conditions, compensation and absenteeism.

    Science.gov (United States)

    Ose, Solveig Osborg

    2005-01-01

    This paper examines absence behaviour in relation to the working environment. A theoretical model is built in order to separate the effects of voluntary absences and absences related to ill health, where health effects are assumed to be tied to working conditions. This model is based on the Shapiro and Stiglitz efficiency wage model. In addition, work environment is introduced as a part of the compensation package. The model gives a testable hypothesis of compensating wage differentials. A panel of quarterly firm level data from 1990 to 1998 are used and the theoretical model is supported by the empirical findings. The result indicates that the workers may not be fully compensated when experiencing high levels of noise in the work area, or when the job involves a high degree of monotonous work, heavy or frequent lifting or poor work postures. Ill health, and thus increased long-term absence, is not highly related to economic variables. However, long-term absence is relatively higher if the firm is troubled with many accidents or near misses. In addition, disamenities for which workers are not fully compensated cause ill health and increased long-term absence.

  10. Psychology of Pay and Compensation

    NARCIS (Netherlands)

    Thierry, Hk.; Smelser, N.J.; Baltes, P.B.

    2002-01-01

    In most industrialized countries the compensation, of managers and employees is structured along quite comparable patterns. One part consists of base pay, a second part of results-oriented pay, and a third part of secondary labor conditions. In many instances part four is composed of perquisites: be

  11. 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.

  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. CEO Compensation in Canada, 1971-2008

    OpenAIRE

    Patrice Gelinas; Lisa Baillargeon

    2013-01-01

    This paper draws from a unique database spanning over 35 years of Canadian CEOs’ compensation to explorethe interplay among: the information available to boards of directors of Canadian companies for makingexecutive pay decisions, the Canadian business environment, and the compensation that Canadian CEOsreceived. We find a very strong correlation between Canadian CEOs’ compensation and the amount ofinformation on CEO compensation available to boards of directors. We further note that the evol...

  15. 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.

  16. Executive Compensation Concentration and Institutional Ownership Power

    OpenAIRE

    Wei Li; Tingting Guo

    2015-01-01

    In this paper, we examine whether institutional shareholders prefer concentrated or dispersed executive compensation structure. To address this question, we study the relationship between executive compensation concentration and institutional ownership power because institutional investors can influence executive compensation more when they have more power. We measure institutional ownership power using institutional ownership level and institutional ownership concentration. We find a signifi...

  17. 16 CFR 16.16 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Compensation. 16.16 Section 16.16 Commercial... MANAGEMENT § 16.16 Compensation. (a) Committee members. Unless otherwise provided by law, the Commission... cost to the Commission. The compensation to be paid to such consultant may not exceed the maximum...

  18. 75 FR 76079 - Sound Incentive Compensation Guidance

    Science.gov (United States)

    2010-12-07

    ... Office of Thrift Supervision Sound Incentive Compensation Guidance AGENCY: Office of Thrift Supervision... collection. Title of Proposal: Sound Incentive Compensation Guidance. OMB Number: 1550-0129. Form Number: N/A... compensation arrangements at a financial institution do not encourage employees to take excessive risks....

  19. 45 CFR 1604.5 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Compensation. 1604.5 Section 1604.5 Public Welfare... Compensation. (a) Except as provided in paragraph (b) of this section and § 1604.7(a), a recipient's written policies shall not permit a full-time attorney to receive any compensation for the outside practice of...

  20. 34 CFR 106.54 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Compensation. 106.54 Section 106.54 Education... Compensation. A recipient shall not make or enforce any policy or practice which, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages...

  1. 6 CFR 17.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Compensation. 17.515 Section 17.515 Domestic... in Employment in Education Programs or Activities Prohibited § 17.515 Compensation. A recipient shall... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a...

  2. 22 CFR 146.515 - Compensation.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Compensation. 146.515 Section 146.515 Foreign... Education Programs or Activities Prohibited § 146.515 Compensation. A recipient shall not make or enforce... compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid...

  3. 32 CFR 196.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 2 2010-07-01 2010-07-01 false Compensation. 196.515 Section 196.515 National... Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one...

  4. 31 CFR 28.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Compensation. 28.515 Section 28.515... Basis of Sex in Employment in Education Programs or Activities Prohibited § 28.515 Compensation. A... in rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex...

  5. 41 CFR 101-4.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 2 2010-07-01 2010-07-01 true Compensation. 101-4.515... Employment in Education Programs or Activities Prohibited § 101-4.515 Compensation. A recipient shall not... pay or other compensation; (b) Results in the payment of wages to employees of one sex at a rate...

  6. 33 CFR 136.113 - Other compensation.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Other compensation. 136.113...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT General Procedure § 136.113 Other compensation....

  7. 45 CFR 618.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Compensation. 618.515 Section 618.515 Public... Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one...

  8. 24 CFR 3.515 - Compensation.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Compensation. 3.515 Section 3.515... Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one...

  9. 10 CFR 5.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Compensation. 5.515 Section 5.515 Energy NUCLEAR... Activities Prohibited § 5.515 Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in...

  10. 45 CFR 86.54 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Compensation. 86.54 Section 86.54 Public Welfare... in Employment in Education Programs or Activities Prohibited § 86.54 Compensation. A recipient shall... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a...

  11. 7 CFR 15a.54 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 1 2010-01-01 2010-01-01 false Compensation. 15a.54 Section 15a.54 Agriculture Office... Activities Prohibited § 15a.54 Compensation. A recipient shall not make or enforce any policy or practice which, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results...

  12. 13 CFR 113.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Compensation. 113.515 Section 113... Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one...

  13. 22 CFR 229.515 - Compensation.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Compensation. 229.515 Section 229.515 Foreign... in Education Programs or Activities Prohibited § 229.515 Compensation. A recipient shall not make or... compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid...

  14. 18 CFR 1317.515 - Compensation.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Compensation. 1317.515... Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one...

  15. 47 CFR 51.221 - Reciprocal compensation.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Reciprocal compensation. 51.221 Section 51.221... Obligations of All Local Exchange Carriers § 51.221 Reciprocal compensation. The rules governing reciprocal compensation are set forth in subpart H of this part....

  16. 7 CFR 301.74-5 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 5 2010-01-01 2010-01-01 false Compensation. 301.74-5 Section 301.74-5 Agriculture..., DEPARTMENT OF AGRICULTURE DOMESTIC QUARANTINE NOTICES Plum Pox § 301.74-5 Compensation. (a) Eligibility. The following individuals are eligible to receive compensation from the U.S. Department of Agriculture...

  17. 75 FR 53023 - Sound Incentive Compensation Guidance

    Science.gov (United States)

    2010-08-30

    ... Office of Thrift Supervision Sound Incentive Compensation Guidance AGENCY: Office of Thrift Supervision... collection. Title of Proposal: Sound Incentive Compensation Guidance. OMB Number: 1550-0129. Form Number: N/A... compensation arrangements at a financial institution do not encourage employees to take excessive risks....

  18. 45 CFR 2555.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Compensation. 2555.515 Section 2555.515 Public... Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one...

  19. 43 CFR 41.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Compensation. 41.515 Section 41.515 Public... in Employment in Education Programs or Activities Prohibited § 41.515 Compensation. A recipient shall... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a...

  20. 48 CFR 836.577 - Workers' compensation.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Workers' compensation. 836.577 Section 836.577 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS SPECIAL...' compensation. The contracting officer shall insert the clause at 852.236-86, Workers' compensation,...

  1. 49 CFR 25.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Compensation. 25.515 Section 25.515 Transportation... Education Programs or Activities Prohibited § 25.515 Compensation. A recipient shall not make or enforce any... compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid...

  2. 14 CFR 1253.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Compensation. 1253.515 Section 1253.515... in Employment in Education Programs or Activities Prohibited § 1253.515 Compensation. A recipient... rates of pay or other compensation; (b) Results in the payment of wages to employees of one sex at...

  3. 77 FR 5381 - Plum Pox Compensation

    Science.gov (United States)

    2012-02-03

    ... Animal and Plant Health Inspection Service 7 CFR Part 301 RIN 0579-AD58 Plum Pox Compensation AGENCY...: We are amending the plum pox regulations to provide for the payment of compensation to eligible owners of non-fruit-bearing ornamental tree nurseries and to increase the amount of compensation that...

  4. Dynamic Phase Compensation of wind turbines

    DEFF Research Database (Denmark)

    Soerensen, P.; Skaarup, J.; Iov, Florin

    2004-01-01

    This paper describes a dynamic phase compensation unit for a wind turbine with directly connected induction generators. The compensation unit is based on thyristor switched capacitors, where conventional wind turbine compensations use mechanical contactors to switch the capacitors. The unit modules...

  5. 40 CFR 5.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Compensation. 5.515 Section 5.515... in Employment in Education Programs or Activities Prohibited § 5.515 Compensation. A recipient shall... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a...

  6. 38 CFR 23.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Compensation. 23.515... Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the payment of wages to employees of one...

  7. 29 CFR 36.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Compensation. 36.515 Section 36.515 Labor Office of the... Activities Prohibited § 36.515 Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results...

  8. 15 CFR 8a.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Compensation. 8a.515 Section 8a.515... in Employment in Education Programs or Activities Prohibited § 8a.515 Compensation. A recipient shall... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a...

  9. 75 FR 22679 - Sound Incentive Compensation Guidance

    Science.gov (United States)

    2010-04-29

    ... Office of Thrift Supervision Sound Incentive Compensation Guidance AGENCY: Office of Thrift Supervision... collection. Title of Proposal: Sound Incentive Compensation Guidance. OMB Number: 1550-0NEW. Form Number: N/A... compensation arrangements at a financial institution do not encourage employees to take excessive risks....

  10. 36 CFR 1211.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Compensation. 1211.515... Prohibited § 1211.515 Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other compensation; (b) Results in the...

  11. 28 CFR 54.515 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Compensation. 54.515 Section 54.515... in Employment in Education Programs or Activities Prohibited § 54.515 Compensation. A recipient shall... of pay or other compensation; (b) Results in the payment of wages to employees of one sex at a...

  12. 33 CFR 5.55 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Compensation. 5.55 Section 5.55 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL COAST GUARD AUXILIARY § 5.55 Compensation. No member of the Auxiliary shall receive any compensation for his services as...

  13. 45 CFR 1607.5 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false Compensation. 1607.5 Section 1607.5 Public Welfare... Compensation. (a) While serving on the governing body of a recipient, no attorney member shall receive compensation from that recipient, but any member may receive a reasonable per diem expense payment...

  14. 7 CFR 1280.208 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Compensation. 1280.208 Section 1280.208 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (MARKETING AGREEMENTS... Board § 1280.208 Compensation. Board members shall serve without compensation, but shall be...

  15. 10 CFR 1042.515 - Compensation.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Compensation. 1042.515 Section 1042.515 Energy DEPARTMENT... Education Programs or Activities Prohibited § 1042.515 Compensation. A recipient shall not make or enforce... compensation; (b) Results in the payment of wages to employees of one sex at a rate less than that paid...

  16. 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

  17. 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.

  18. 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.

  19. 76 FR 37897 - Performance of Functions; Claims for Compensation Under the Federal Employees' Compensation Act...

    Science.gov (United States)

    2011-06-28

    ..., Office of Workers' Compensation Programs, Federal Employees' Compensation Act File, 67 FR 16826 (April 8... Office of Workers' Compensation Programs (OWCP) by Employment Standards Order No. 2-74 (39 FR 34722). The... Programs (37 FR 20533) and an Office of Federal Employees' Compensation (37 FR 22979). In 1974, these...

  20. Bank Efficiency and Executive Compensation

    OpenAIRE

    Timothy King; Jonathan Williams

    2013-01-01

    We investigate whether handsomely rewarding bank executives’ realizes superior efficiency by determining if executive remuneration contracts produce incentives that offset potential agency problems and lead to improvements in bank efficiency. We calculate executive Delta and Vega to proxy executives’ risk-taking following changes in their compensation contracts and estimate their relationship with alternative profit efficiency. Our study uses novel instruments to account for the potentially e...

  1. Compensating Differentials for Sexual Harassment

    OpenAIRE

    Joni Hersch

    2011-01-01

    Workplace sexual harassment is illegal, but many workers report that they have been sexually harassed. Exposure to the risk of sexual harassment may decrease productivity, which would reduce wages. Alternatively, workers may receive a compensating differential for exposure to sexual harassment, which would increase wages. Data on claims of sexual harassment filed with the Equal Employment Opportunity Commission are used to calculate the first measures of sexual harassment risks by industry, a...

  2. Has compensation become more flexible?

    OpenAIRE

    Sandra A. Cannon; Bruce C. Fallick; Michael Lettau; Raven E. Saks

    2000-01-01

    In recent years, numerous observers have argued that global competition, increased reliance on contingent workers, and the breakdown of implicit contracts have made compensation practices in the United States more flexible; in particular, employers have become more concerned with how an employee's pay compares to that in other firms and less concerned with considerations of equity or relative pay within the firm. This paper uses establishment-level data from the Bureau of Labor Statistics' Em...

  3. 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.

  4. 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...

  5. Space Tug Docking Study. Volume 5: Cost Analysis

    Science.gov (United States)

    1976-01-01

    The cost methodology, summary cost data, resulting cost estimates by Work Breakdown Structure (WBS), technical characteristics data, program funding schedules and the WBS for the costing are discussed. Cost estimates for two tasks of the study are reported. The first, developed cost estimates for design, development, test and evaluation (DDT&E) and theoretical first unit (TFU) at the component level (Level 7) for all items reported in the data base. Task B developed total subsystem DDT&E costs and funding schedules for the three candidate Rendezvous and Docking Systems: manual, autonomous, and hybrid.

  6. Docking study of HIV-1 reverse transcriptase with phytochemicals.

    Science.gov (United States)

    Seal, Abhik; Aykkal, Riju; Babu, Rosana O; Ghosh, Mriganka

    2011-02-15

    Natural products are important sources of drug discovery. In this context groups of different set of phytochemicals were taken and docked into the different cavities of the Reverse transcriptase (PDB ID: 1REV) of Human immunodeficiency virus (HIV) and results were discussed. Natural compounds such as Curcumin, Geranin, Gallotannin, Tiliroside, Kaempferol-3-o-glucoside and Trachelogenin were found to very effective according to its binding energy and ligand efficiency score. Those compounds also were found to have no adverse effect as carcinogenicity and mutagenicity and favorable drug likeness score. Hence, considering the facts those compounds could use effectively for HIV-1 drug discovery.

  7. Synthesis, antiproliferative activity and molecular docking of Colchicine derivatives.

    Science.gov (United States)

    Huczyński, Adam; Majcher, Urszula; Maj, Ewa; Wietrzyk, Joanna; Janczak, Jan; Moshari, Mahshad; Tuszynski, Jack A; Bartl, Franz

    2016-02-01

    In order to create more potent anticancer agents, a series of five structurally different derivatives of Colchicine have been synthesised. These compounds were characterised spectroscopically and structurally and their antiproliferative activity against four human tumour cell lines (HL-60, HL-60/vinc, LoVo, LoVo/DX) was evaluated. Additionally the activity of the studied compounds was calculated using computational methods involving molecular docking of the Colchicine derivatives to β-tubulin. The experimental and computational results are in very good agreement indicating that the antimitotic activity of Colchicine derivatives can be readily predicted using computational modeling methods.

  8. Compensation Techniques in Accelerator Physics

    Energy Technology Data Exchange (ETDEWEB)

    Sayed, Hisham Kamal [Old Dominion Univ., Norfolk, VA (United States)

    2011-05-01

    Accelerator physics is one of the most diverse multidisciplinary fields of physics, wherein the dynamics of particle beams is studied. It takes more than the understanding of basic electromagnetic interactions to be able to predict the beam dynamics, and to be able to develop new techniques to produce, maintain, and deliver high quality beams for different applications. In this work, some basic theory regarding particle beam dynamics in accelerators will be presented. This basic theory, along with applying state of the art techniques in beam dynamics will be used in this dissertation to study and solve accelerator physics problems. Two problems involving compensation are studied in the context of the MEIC (Medium Energy Electron Ion Collider) project at Jefferson Laboratory. Several chromaticity (the energy dependence of the particle tune) compensation methods are evaluated numerically and deployed in a figure eight ring designed for the electrons in the collider. Furthermore, transverse coupling optics have been developed to compensate the coupling introduced by the spin rotators in the MEIC electron ring design.

  9. 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.

  10. 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

  11. PMD compensation based on a new type dynamic first-order PMD compensator

    Institute of Scientific and Technical Information of China (English)

    Jiajun Wang; Shilong Pan; Jia Jia; Yanfu Yang; Caiyun Lou

    2006-01-01

    @@ A dynamic first-order polarization mode dispersion (PMD) compensator based on garnet and yttrium vanadate crystal has been proposed and implemented. Consisting of a differential group delay (DGD) generator and a Faraday rotator (FR), this PMD compensator has only two degrees of freedom. Feedback control and compensation algorithm are both very simple. Experimental results reveal the compensator behaviors to be excellent for PMD compensation in 40-Gb/s optical time domain multiplexing (OTDM)system.

  12. 78 FR 68867 - Division of Longshore and Harbor Workers' Compensation

    Science.gov (United States)

    2013-11-15

    ... of Workers' Compensation Programs Division of Longshore and Harbor Workers' Compensation Proposed... Office of Workers' Compensation (OWCP) is soliciting comments concerning the proposed collection...). SUPPLEMENTARY INFORMATION: I. Background: The Office of Workers' Compensation Programs, (OWCP) administers...

  13. Docks and Piers, Port of Green Bay docks along the Fox River are complete, Published in 2008, 1:1200 (1in=100ft) scale, Brown County, WI.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Docks and Piers dataset, published at 1:1200 (1in=100ft) scale, was produced all or in part from Orthoimagery information as of 2008. It is described as 'Port...

  14. DOCK8 deficiency impairs CD8 T cell survival and function in humans and mice

    Science.gov (United States)

    Randall, Katrina L.; Chan, Stephanie S.-Y.; Ma, Cindy S.; Fung, Ivan; Mei, Yan; Yabas, Mehmet; Tan, Andy; Arkwright, Peter D.; Al Suwairi, Wafaa; Lugo Reyes, Saul Oswaldo; Yamazaki-Nakashimada, Marco A.; de la Luz Garcia-Cruz, Maria; Smart, Joanne M.; Picard, Capucine; Okada, Satoshi; Jouanguy, Emmanuelle; Casanova, Jean-Laurent; Lambe, Teresa; Cornall, Richard J.; Russell, Sarah; Oliaro, Jane; Tangye, Stuart G.; Bertram, Edward M.

    2011-01-01

    In humans, DOCK8 immunodeficiency syndrome is characterized by severe cutaneous viral infections. Thus, CD8 T cell function may be compromised in the absence of DOCK8. In this study, by analyzing mutant mice and humans, we demonstrate a critical, intrinsic role for DOCK8 in peripheral CD8 T cell survival and function. DOCK8 mutation selectively diminished the abundance of circulating naive CD8 T cells in both species, and in DOCK8-deficient humans, most CD8 T cells displayed an exhausted CD45RA+CCR7− phenotype. Analyses in mice revealed the CD8 T cell abnormalities to be cell autonomous and primarily postthymic. DOCK8 mutant naive CD8 T cells had a shorter lifespan and, upon encounter with antigen on dendritic cells, exhibited poor LFA-1 synaptic polarization and a delay in the first cell division. Although DOCK8 mutant T cells underwent near-normal primary clonal expansion after primary infection with recombinant influenza virus in vivo, they showed greatly reduced memory cell persistence and recall. These findings highlight a key role for DOCK8 in the survival and function of human and mouse CD8 T cells. PMID:22006977

  15. Connecting in Space: Docking with the International Space Station. Educational Brief.

    Science.gov (United States)

    National Aeronautics and Space Administration, Washington, DC.

    This brief discusses the space shuttle and the docking procedures used with the International Space Station (ISS). Using this activity designed for grades 5-12, students demonstrate and identify procedures for determining the best method for completing the docking activity. Students will also study and identify Newton's Laws of Motion. A mockup…

  16. 75 FR 38831 - Repair Kalaupapa Dock Structure: Kalaupapa National Historical Park, Hawaii; Notice of...

    Science.gov (United States)

    2010-07-06

    ... National Park Service Repair Kalaupapa Dock Structure: Kalaupapa National Historical Park, Hawaii; Notice... Impact Statement (EIS) as previously noticed in the Federal Register on April 17, 2009, for repair of... environmental consequences of the proposed dock repairs, including minor to moderate effects on water...

  17. DOCK8 Deficiency : Clinical and Immunological Phenotype and Treatment Options - a Review of 136 Patients

    NARCIS (Netherlands)

    Aydin, Susanne E.; Kilic, Sara Sebnem; Aytekin, Caner; Kumar, Ashish; Porras, Oscar; Kainulainen, Leena; Kostyuchenko, Larysa; Genel, Ferah; Kutukculer, Necil; Karaca, Neslihan; Gonzalez-Granado, Luis; Abbott, Jordan; Al-Zahrani, Daifulah; Rezaei, Nima; Baz, Zeina; Thiel, Jens; Ehl, Stephan; Marodi, Laszlo; Orange, Jordan S.; Sawalle-Belohradsky, Julie; Keles, Sevgi; Holland, Steven M.; Sanal, Ozden; Ayvaz, Deniz C.; Tezcan, Ilhan; Al-Mousa, Hamoud; Alsum, Zobaida; Hawwari, Abbas; Metin, Ayse; Matthes-Martin, Susanne; Hoenig, Manfred; Schulz, Ansgar; Picard, Capucine; Barlogis, Vincent; Gennery, Andrew; Ifversen, Marianne; van Montfrans, JM; Kuijpers, Taco; Bredius, Robbert; Duckers, Gregor; Al-Herz, Waleed; Pai, Sung-Yun; Geha, Raif; Notheis, Gundula; Schwarze, Carl-Philipp; Tavil, Betul; Azik, Fatih; Bienemann, Kirsten; Grimbacher, Bodo; Heinz, Valerie; Gaspar, H. Bobby; Aydin, Roland; Hagl, Beate; Gathmann, Benjamin; Belohradsky, Bernd H.; Ochs, Hans D.; Chatila, Talal; Renner, Ellen D.; Su, Helen; Freeman, Alexandra F.; Engelhardt, Karin; Albert, Michael H.

    2015-01-01

    Mutations in DOCK8 result in autosomal recessive Hyper-IgE syndrome with combined immunodeficiency (CID). However, the natural course of disease, long-term prognosis, and optimal therapeutic management have not yet been clearly defined. In an international retrospective survey of patients with DOCK8

  18. 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

  19. 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)...

  20. 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;

    2012-01-01

    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...

  1. 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

  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. 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.

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. DC-Compensated Current Transformer.

    Science.gov (United States)

    Ripka, Pavel; Draxler, Karel; Styblíková, Renata

    2016-01-01

    Instrument current transformers (CTs) measure AC currents. The DC component in the measured current can saturate the transformer and cause gross error. We use fluxgate detection and digital feedback compensation of the DC flux to suppress the overall error to 0.15%. This concept can be used not only for high-end CTs with a nanocrystalline core, but it also works for low-cost CTs with FeSi cores. The method described here allows simultaneous measurements of the DC current component. PMID:26805830

  10. DC-Compensated Current Transformer.

    Science.gov (United States)

    Ripka, Pavel; Draxler, Karel; Styblíková, Renata

    2016-01-20

    Instrument current transformers (CTs) measure AC currents. The DC component in the measured current can saturate the transformer and cause gross error. We use fluxgate detection and digital feedback compensation of the DC flux to suppress the overall error to 0.15%. This concept can be used not only for high-end CTs with a nanocrystalline core, but it also works for low-cost CTs with FeSi cores. The method described here allows simultaneous measurements of the DC current component.

  11. MOLS 2.0: software package for peptide modeling and protein-ligand docking.

    Science.gov (United States)

    Paul, D Sam; Gautham, N

    2016-10-01

    We previously developed an algorithm to perform conformational searches of proteins and peptides, and to perform the docking of ligands to protein receptors. In order to identify optimal conformations and docked poses, this algorithm uses mutually orthogonal Latin squares (MOLS) to rationally sample the vast conformational (or docking) space, and then analyzes this relatively small sample using a variant of mean field theory. The conformational search part of the algorithm was denoted MOLS 1.0. The docking portion of the algorithm, which allows only "flexible ligand/rigid receptor" docking, was denoted MOLSDOCK. Both are FORTRAN-based command-line-only molecular docking computer programs, though a GUI was developed later for MOLS 1.0. Both the conformational search and the rigid receptor docking parts of the algorithm have been extensively validated. We have now further enhanced the capabilities of the program by incorporating "induced fit" side-chain receptor flexibility for docking peptide ligands. Benchmarking and extensive testing is now being carried out for the flexible receptor portion of the docking. Additionally, to make both the peptide conformational search and docking algorithms (the latter including both flexible ligand/rigid receptor and flexible ligand/flexible receptor techniques) more accessible to the research community, we have developed MOLS 2.0, which incorporates a new Java-based graphical user interface (GUI). Here, we give a detailed description of MOLS 2.0. The source code and binary for MOLS 2.0 are distributed free (under a GNU Lesser General Public License) to the scientific community. They are freely available for download at https://sourceforge.net/projects/mols2-0/files/ . PMID:27638416

  12. MOLS 2.0: software package for peptide modeling and protein-ligand docking.

    Science.gov (United States)

    Paul, D Sam; Gautham, N

    2016-10-01

    We previously developed an algorithm to perform conformational searches of proteins and peptides, and to perform the docking of ligands to protein receptors. In order to identify optimal conformations and docked poses, this algorithm uses mutually orthogonal Latin squares (MOLS) to rationally sample the vast conformational (or docking) space, and then analyzes this relatively small sample using a variant of mean field theory. The conformational search part of the algorithm was denoted MOLS 1.0. The docking portion of the algorithm, which allows only "flexible ligand/rigid receptor" docking, was denoted MOLSDOCK. Both are FORTRAN-based command-line-only molecular docking computer programs, though a GUI was developed later for MOLS 1.0. Both the conformational search and the rigid receptor docking parts of the algorithm have been extensively validated. We have now further enhanced the capabilities of the program by incorporating "induced fit" side-chain receptor flexibility for docking peptide ligands. Benchmarking and extensive testing is now being carried out for the flexible receptor portion of the docking. Additionally, to make both the peptide conformational search and docking algorithms (the latter including both flexible ligand/rigid receptor and flexible ligand/flexible receptor techniques) more accessible to the research community, we have developed MOLS 2.0, which incorporates a new Java-based graphical user interface (GUI). Here, we give a detailed description of MOLS 2.0. The source code and binary for MOLS 2.0 are distributed free (under a GNU Lesser General Public License) to the scientific community. They are freely available for download at https://sourceforge.net/projects/mols2-0/files/ .

  13. 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

  14. 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

  15. Vertical vibration analysis for elevator compensating sheave

    International Nuclear Information System (INIS)

    Most elevators applied to tall buildings include compensating ropes to satisfy the balanced rope tension between the car and the counter weight. The compensating ropes receive tension by the compensating sheave, which is installed at the bottom space of the elevator shaft. The compensating sheave is only suspended by the compensating ropes, therefore, the sheave can move vertically while the car is traveling. This paper shows the elevator dynamic model to evaluate the vertical motion of the compensating sheave. Especially, behavior in emergency cases, such as brake activation and buffer strike, was investigated to evaluate the maximum upward motion of the sheave. The simulation results were validated by experiments and the most influenced factor for the sheave vertical motion was clarified

  16. Pointing compensation system for spacecraft instruments

    Science.gov (United States)

    Plescia, Carl T. (Inventor); Gamble, Donald W. (Inventor)

    1987-01-01

    A closed loop system reduces pointing errors in one or more spacecraft instruments. Associated with each instrument is a electronics package (3) for commanding motion in that instrument and a pointing control system (5) for imparting motion in that instrument in response to a command (4) from the commanding package (3). Spacecraft motion compensation logic (25) compensates for instrument pointing errors caused by instrument-motion-induced spacecraft motion. Any finite number of instruments can be so compensated, by providing each pointing control system (5) and each commanding package (3), for the instruments desired to be compensated, with a link to the spacecraft motion compensation logic (25). The spacecraft motion compensation logic (25) is an electronic manifestation of the algebraic negative of a model of the dynamics of motion of the spacecraft. An example of a suitable model, and computer-simulated results, are presented.

  17. A New Interpretation of Compensate Effect

    CERN Document Server

    Shao, M X

    2000-01-01

    A new interpretation of compensate effect is presented. The Hawking effect in general space-time can be taken as a compensate effect of the scale transformation of coordinate time on the horizon in generalized tortoise coordinates transformation. It is proved that the Hawking temperature is the pure gauge of compensate field in tortoise coordinates. This interpretation does not refer to a zero-temperature space-time.

  18. Compensation consultants and CEO pay: UK evidence

    OpenAIRE

    Voulgaris, Georgios; Stathopoulos, Konstantinos; Walker, Martin

    2010-01-01

    International audience Manuscript type: Empirical Research Question/ Issue: This paper provides new evidence on the effect of compensation consultants on CEO pay. Research Findings/ Insights: We produce new evidence on the managerial power approach (MPA) to corporate governance by examining the influence of compensation consultants on CEO pay structures and the decision to hire a compensation consultant in the UK. We find evidence that is not consistent with the MPA. Contrary to the MPA pr...

  19. Compensation for earnings risk under worker heterogeneity

    OpenAIRE

    Berkhout, P.; Hartog, J.; Webbink, D.

    2006-01-01

    We use two large Dutch datasets to estimate the Risk Augmented Mincer equation and test for risk compensation in expected earnings. We replicate earlier findings of a positive premium for risk and a negative premium for skew and add confirmation of the key results if we control for individual ability. We find that immigrants have graduated in more risky educations but obtain identical risk compensation. Among recent graduates, women receive higher risk compensation than men, consistent with t...

  20. Securitization and Compensation in Financial Institutions

    OpenAIRE

    Inderst, Roman; Pfeil, Sebastian

    2010-01-01

    We analyze the interaction between financial institutions' internal compensation policy, the quality of loans, and their securitization decision. We also assess the case for requiring financial institutions to defer bonus pay so as to make incentives more commensurate with the longer-term risk of their transactions. While mandatory deferred compensation can improve the quality of loans, we also show when it has the opposite effect. We further analyze when mandatory deferred compensation can c...

  1. Extended frequency compensation of a diamagnetic loop

    International Nuclear Information System (INIS)

    A method of compensation for a diamagnetic loop that is magnetically coupled to a concentric stainless-steel vacuum vessel is presented. This compensation method accounts for imperfect magnetic coupling between the vessel eddy currents, the diamagnetic loop, and the plasma diamagnetic currents, and it also corrects for a finite loading resistance on the diamagnetic loop. A procedure for adjusting and calibrating the active-filter compensation circuit is presented. It can be applied to internal or external diamagnetic loops. (author)

  2. Employee Sentiment and Stock Option Compensation

    OpenAIRE

    Nittai K. Bergman; Dirk Jenter

    2005-01-01

    The use of equity-based compensation for employees in the lower ranks of large organizations is a puzzle for standard economic theory: undiversified employees should discount company equity heavily, and any positive incentive effects should be diminished by free rider problems. We analyze whether the popularity of option compensation for rank and file employees may be driven by employee optimism. We develop a model of optimal compensation policy for a firm faced with employees with positive o...

  3. 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.

  4. Mortality among dock-yard workers in Genoa, Italy.

    Science.gov (United States)

    Puntoni, R; Russo, L; Zannini, D; Vercelli, M; Gambaro, R P; Valerio, F; Santi, L

    1977-01-01

    The causes of death among the dock-yard workers of Genoa from December 31, 1959 to January 1, 1970, have been investigated. These workers, mainly assigned to ship repair, refitting and construction, are exposed to several noxious substances, such as: asbestos, silica, paint solvents, welding smoke and volatile products of petroleum. Two different control groups were selected: the male population of Genoa and the staff of the San Martino Hospital in Genoa. Causes of death showing a significant increase were: gastric cancer (only in comparison with the hospital staff), cancer of colon excluding rectum, lung cancer, cancer of kidney, urinary bladder and other urinary organs, respiratory diseases, cirrhosis of the liver, cardiovascular diseases (only in comparison with the hospital staff).

  5. 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.

  6. 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.

  7. Broadband dispersion compensation using microstructure fibers

    Institute of Scientific and Technical Information of China (English)

    Xia Zhang; Xiaomin Ren; Yongzhao Xu; Zinan Wang; Yongqing Huang; Xue Chen

    2007-01-01

    Beijing University of Posts and Telecommunications, Beijing 100876Dispersion and dispersion slope compensation of 10-Gb/s pulses using microstructure fibers (MFs) is demonstrated experimentally. A 26-m MF is used to compensate the dispersion of 2-km standard singe mode fiber in a 20-nm range in C band. The experimental results show that a significant improvement can be achieved in the quality of the observed pulses with the dispersion compensation. Moreover, the further research shows that the MF can compensate the anomalous dispersion of a single mode fiber within ±0.27 ps/(nm·km) over a 50-nm wavelength range from 1520 to 1570 nm.

  8. Lithium compensation for full cell operation

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jie; Zheng, Jianming; Chen, Xilin; Lu, Dongping; Liu, Jun; Jiguang, Jiguang

    2016-05-17

    Disclosed herein are embodiments of a lithium-ion battery system comprising an anode, an anode current collector, and a layer of lithium metal in contact with the current collector, but not in contact with the anode. The lithium compensation layer dissolves into the electrolyte to compensate for the loss of lithium ions during usage of the full cell. The specific placement of the lithium compensation layer, such that there is no direct physical contact between the lithium compensation layer and the anode, provides certain advantages.

  9. Log amplifier with pole-zero compensation

    Science.gov (United States)

    Brookshier, William

    1987-01-01

    A logarithmic amplifier circuit provides pole-zero compensation for improved stability and response time over 6-8 decades of input signal frequency. The amplifier circuit includes a first operational amplifier with a first feedback loop which includes a second, inverting operational amplifier in a second feedback loop. The compensated output signal is provided by the second operational amplifier with the log elements, i.e., resistors, and the compensating capacitors in each of the feedback loops having equal values so that each break point or pole is offset by a compensating break point or zero.

  10. Enthalpy-entropy compensation in protein unfolding

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin of the enthalpy-entropy compensation in protein unfolding. It is indicated that the enthalpy-entropy compensation constitutes the physical foundation that satisfies the biological need of the small free energy changes in protein unfolding, without the sacrifice of the bio-diversity of proteins. The enthalpy-entropy compensation theory proposed herein also provides valuable insights into the Privalov's puzzle of enthalpy and entropy convergence in protein unfolding.

  11. Undulator with dynamic compensation of magnetic forces

    Energy Technology Data Exchange (ETDEWEB)

    Gluskin, Efim; Trakhtenberg, Emil; Xu, Joseph Z.

    2016-05-31

    A method and apparatus for implementing dynamic compensation of magnetic forces for undulators are provided. An undulator includes a respective set of magnet arrays, each attached to a strongback, and placed on horizontal slides and positioned parallel relative to each other with a predetermined gap. Magnetic forces are compensated by a set of compensation springs placed along the strongback. The compensation springs are conical springs having exponential-force characteristics that substantially match undulator magnetic forces independently of the predetermined gap. The conical springs are positioned along the length of the magnets.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. Pharmacophore Modeling and Molecular Docking Studies on Pinus roxburghii as a Target for Diabetes Mellitus.

    Science.gov (United States)

    Kaushik, Pawan; Lal Khokra, Sukhbir; Rana, A C; Kaushik, Dhirender

    2014-01-01

    The present study attempts to establish a relationship between ethnopharmacological claims and bioactive constituents present in Pinus roxburghii against all possible targets for diabetes through molecular docking and to develop a pharmacophore model for the active target. The process of molecular docking involves study of different bonding modes of one ligand with active cavities of target receptors protein tyrosine phosphatase 1-beta (PTP-1β), dipeptidyl peptidase-IV (DPP-IV), aldose reductase (AR), and insulin receptor (IR) with help of docking software Molegro virtual docker (MVD). From the results of docking score values on different receptors for antidiabetic activity, it is observed that constituents, namely, secoisoresinol, pinoresinol, and cedeodarin, showed the best docking results on almost all the receptors, while the most significant results were observed on AR. Then, LigandScout was applied to develop a pharmacophore model for active target. LigandScout revealed that 2 hydrogen bond donors pointing towards Tyr 48 and His 110 are a major requirement of the pharmacophore generated. In our molecular docking studies, the active constituent, secoisoresinol, has also shown hydrogen bonding with His 110 residue which is a part of the pharmacophore. The docking results have given better insights into the development of better aldose reductase inhibitor so as to treat diabetes related secondary complications. PMID:25114678

  18. Pharmacophore Modeling and Molecular Docking Studies on Pinus roxburghii as a Target for Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    Pawan Kaushik

    2014-01-01

    Full Text Available The present study attempts to establish a relationship between ethnopharmacological claims and bioactive constituents present in Pinus roxburghii against all possible targets for diabetes through molecular docking and to develop a pharmacophore model for the active target. The process of molecular docking involves study of different bonding modes of one ligand with active cavities of target receptors protein tyrosine phosphatase 1-beta (PTP-1β, dipeptidyl peptidase-IV (DPP-IV, aldose reductase (AR, and insulin receptor (IR with help of docking software Molegro virtual docker (MVD. From the results of docking score values on different receptors for antidiabetic activity, it is observed that constituents, namely, secoisoresinol, pinoresinol, and cedeodarin, showed the best docking results on almost all the receptors, while the most significant results were observed on AR. Then, LigandScout was applied to develop a pharmacophore model for active target. LigandScout revealed that 2 hydrogen bond donors pointing towards Tyr 48 and His 110 are a major requirement of the pharmacophore generated. In our molecular docking studies, the active constituent, secoisoresinol, has also shown hydrogen bonding with His 110 residue which is a part of the pharmacophore. The docking results have given better insights into the development of better aldose reductase inhibitor so as to treat diabetes related secondary complications.

  19. A new compensator at CERN

    CERN Document Server

    Kahle, K

    2005-01-01

    In 2001 a first Static Var Compensator (SVC) based on a set of thyristor-controlled reactors was commissioned for the SPS. This was the first step in the process of replacing the obsolete saturated reactors installed in the early seventies. The second step is now in preparation: dismantling of the so-called “North compensator” and replacing it with a second SVC, essentially identical to the one commissioned in 2001. This paper describes the project and its consequences for the operation of the 400/18 kV main substation. The paper describes briefly the recuperation of certain existing components, civil engineering and other hardware. Finally a budget estimation and the planning are presented.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 76 FR 6009 - Shareholder Approval of Executive Compensation and Golden Parachute Compensation

    Science.gov (United States)

    2011-02-02

    ... Item 20 of Schedule 14A; TARP Adopting Release, supra note 18, at 75 FR 2790. b. Comments on the... Executive Compensation and Golden Parachute Compensation; Final Rule #0;#0;Federal Register / Vol. 76, No... 17 CFR Parts 229, 240 and 249 RIN 3235-AK68 Shareholder Approval of Executive Compensation and...

  5. 38 CFR 3.351 - Special monthly dependency and indemnity compensation, death compensation, pension and spouse's...

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Special monthly dependency and indemnity compensation, death compensation, pension and spouse's compensation ratings. 3.351 Section 3.351 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS ADJUDICATION...

  6. 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

  7. 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

  8. Ligand-protein docking using a quantum stochastic tunneling optimization method.

    Science.gov (United States)

    Mancera, Ricardo L; Källblad, Per; Todorov, Nikolay P

    2004-04-30

    A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.

  9. 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...

  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. 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...

  12. 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.

  13. Tilt/Integral/Derivative Compensators For Controllers

    Science.gov (United States)

    Lurie, Boris J.

    1995-01-01

    Tilt/integral/derivative (TID) compensators for tunable feedback control systems offer advantages over proportional/integral/derivative compensators. Designed and adjusted more easily, and made to reject disturbances more strongly and less sensitive to variations in parameters of controlled system.

  14. Springback Compensation: Fundamental Topics and Practical Application

    NARCIS (Netherlands)

    Lingbeek, R.; Meinders, T.; Ohnimus, S.; Petzoldt, M.; Weiher, J.

    2006-01-01

    Now that the simulation of deep drawing processes has become more reliable the virtual compensation of the forming tools has become reality. In literature, the Displacement Adjustment (DA) algorithm has proved to be most effective. In this article it is shown how the compensation factor, required fo

  15. A brief history of dosage compensation

    Indian Academy of Sciences (India)

    Stanley M. Gartler

    2014-08-01

    In 1914, H. J. Muller postulated the origin of the Y chromosome as having resulted from restricted recombination between homologous sex chromosomes in the male and the accumulation of deleterious mutations. This evolutionary process leads to dosage compensation. This article lays out a brief history of dosage compensation in genetics.

  16. 45 CFR 63.35 - Dual compensation.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Dual compensation. 63.35 Section 63.35 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION GRANT PROGRAMS ADMINISTERED BY THE... compensation. If a project staff member or consultant of one grantee is involved simultaneously in two or...

  17. 28 CFR 345.54 - Overtime compensation.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Overtime compensation. 345.54 Section 345.54 Judicial Administration FEDERAL PRISON INDUSTRIES, INC., DEPARTMENT OF JUSTICE FEDERAL PRISON INDUSTRIES (FPI) INMATE WORK PROGRAMS Inmate Pay and Benefits § 345.54 Overtime compensation. An...

  18. 7 CFR 930.61 - Handler compensation.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Handler compensation. 930.61 Section 930.61 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing... Handling Regulations § 930.61 Handler compensation. Each handler handling cherries from a...

  19. 33 CFR 136.205 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.205...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.205...

  20. 33 CFR 136.241 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.241...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.241...

  1. 33 CFR 136.235 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.235...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.235...

  2. Individual Hearing Loss: Characterization, Modelling, Compensation Strategies

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Dau, Torsten; Christensen-Dalsgaard, Jakob;

    2016-01-01

    account for such individual differences, which make it challenging to find adequate compensation strategies in hearing devices. How to characterize, model, and compensate for individual hearing loss were the main topics of the fifth International Symposium on Auditory and Audiological Research (ISAAR...

  3. 44 CFR 19.515 - Compensation.

    Science.gov (United States)

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Compensation. 19.515 Section... Programs or Activities Prohibited § 19.515 Compensation. A recipient shall not make or enforce any policy or practice that, on the basis of sex: (a) Makes distinctions in rates of pay or other...

  4. 33 CFR 136.229 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.229...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.229...

  5. 33 CFR 136.211 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.211...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.211...

  6. 33 CFR 136.217 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.217...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.217...

  7. 28 CFR 34.111 - Compensation.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Compensation. 34.111 Section 34.111 Judicial Administration DEPARTMENT OF JUSTICE OJJDP COMPETITION AND PEER REVIEW PROCEDURES Peer Review § 34.111 Compensation. All peer reviewers will be eligible to be paid according to applicable...

  8. 24 CFR 964.340 - Resident compensation.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Resident compensation. 964.340 Section 964.340 Housing and Urban Development Regulations Relating to Housing and Urban Development...) Program § 964.340 Resident compensation. Residents employed to provide services or renovation...

  9. 33 CFR 136.223 - Compensation allowable.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Compensation allowable. 136.223...) MARINE POLLUTION FINANCIAL RESPONSIBILITY AND COMPENSATION OIL SPILL LIABILITY TRUST FUND; CLAIMS PROCEDURES; DESIGNATION OF SOURCE; AND ADVERTISEMENT Procedures for Particular Claims § 136.223...

  10. Multiple Compensation Consultants and CEO Pay

    NARCIS (Netherlands)

    Kabir, Rezaul; Minhat, Marizah

    2010-01-01

    The study examines the practice of employing multiple compensation consultants. Data for a sample of UK companies over the period 2003-2006 are analyzed using a variety of econometric methods. We find that CEOs receive higher equity-based pay when firms employ more than one compensation consultant.

  11. Motion compensator for holographic motion picture camera

    Science.gov (United States)

    Kurtz, R. L.

    1973-01-01

    When reference beam strikes target it undergoes Doppler shift dependent upon target velocity. To compensate, object beam is first reflected from rotating cylinder that revolves in direction opposite to target but at same speed. When beam strikes target it is returned to original frequency and is in phase with reference beam. Alternatively this motion compensator may act on reference beam.

  12. 20 CFR 211.15 - Verification of compensation claimed.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Verification of compensation claimed. 211.15... CREDITABLE RAILROAD COMPENSATION § 211.15 Verification of compensation claimed. Compensation claimed by an... Board before it may be credited. An employee's claim to compensation not credited shall be processed...

  13. 20 CFR 211.2 - Definition of compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Definition of compensation. 211.2 Section 211... CREDITABLE RAILROAD COMPENSATION § 211.2 Definition of compensation. (a) The term compensation means any form... termination allowance paid under section 702 of that Act. Compensation may be paid as money, a commodity,...

  14. 20 CFR 211.14 - Maximum creditable compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Maximum creditable compensation. 211.14... CREDITABLE RAILROAD COMPENSATION § 211.14 Maximum creditable compensation. Maximum creditable compensation... Employment Accounts shall notify each employer of the amount of maximum creditable compensation applicable...

  15. 20 CFR 226.62 - Computing average monthly compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Computing average monthly compensation. 226... Compensation § 226.62 Computing average monthly compensation. The employee's average monthly compensation is computed by first determining the employee's highest 60 months of railroad compensation...

  16. Ownership Concentration, Top Management and Board Compensation

    Directory of Open Access Journals (Sweden)

    Marcos Barbosa Pinto

    2013-05-01

    Full Text Available The degree of ownership concentration may influence executive and board compensation (Bebchuk & Fried, 2003. This article analyzes this relationship. Detailed information about top management and board compensation became available starting in 2010 through new Securities Commission filings. Linear regression models applied to a sample of 315 Brazilian companies traded on the national exchange indicate a negative and statistically significant economic correlation between executive compensation and the degree of ownership concentration. Ceteris paribus, companies with a lower degree of ownership concentration pay higher compensation to top executives. Family controlled companies pay more to their chief executive, but not to the managerial team as a whole, and the compensation of directors increases with a greater proportion of control group members or their relatives on the board. There was support for the Managerial Power Hypothesis in companies with a lower degree of ownership concentration and for the extraction of private benefits in companies where it is greater.

  17. Compensating large PMD by a fiber grating

    Institute of Scientific and Technical Information of China (English)

    Tangjun Li(李唐军); Muguang Wang(王目光); Cao Diao(刁操); Shuisheng Jian(简水生)

    2004-01-01

    In this paper, the first- and second-order polarization mode dispersion (PMD) with the amount of 132.994-ps differential group-delay (DGD) and maximum 476.129-ps/nm second-order PMD can be compensated by a two-stages PMD compensator at a 40-Gb/s optical fiber communication system. The first stage has one free degree that is used for first order and high orders PMD compensations by rotating the state of polarization. The second-stage is used for remainder PMD compensations. After compensation, the average DGD and the maximum second-order PMD are reduced to 345.310 fs and 3.102 ps/nm, respectively.

  18. Rectangular Laser Resonators with Astigmatic Compensation

    DEFF Research Database (Denmark)

    Skettrup, Torben

    2005-01-01

    An investigation of rectangular resonators with a view to the compensation of astigmatism has been performed. In order to have beam waists placed at the same positions in the tangential and sagittal planes, pairs of equal mirrors were considered. It was found that at least two concave mirrors...... are necessary to obtain compensation. Four-concave-mirror systems are most stable close to the quadratic geometry, although the symmetric quadratic resonator itself cannot be compensated for astigmatism. Using four equal concave mirrors, compensation of astigmatism can be obtained in two arms at the same time....... Usually several stability ranges are found for four-mirror resonators with pair-wise equal mirrors, and it is possible with these systems to obtain small compensated beam waist radii suitable for frequency conversion. Relevant formulae are given and several relevant examples are shown using simulation...

  19. Engineering Compensations in Web Service Environment

    DEFF Research Database (Denmark)

    Schäfer, Micahel; Dolog, Peter; Nejdl, Wolfgang

    2007-01-01

    Business to business integration has recently been performed by employing Web service environments. Moreover, such environments are being provided by major players on the technology markets. Those environments are based on open specifications for transaction coordination. When a failure...... in such an environment occurs, a compensation can be initiated to recover from the failure. However, current environments have only limited capabilities for compensations, and are usually based on backward recovery. In this paper, we introduce an engineering approach and an environment to deal with advanced...... introduce the abstract service and adapter components which allow us to separate the compensation logic from the coordination logic. In this way, we can easily plug in or plug out different compensation strategies based on a specification language defined on top of basic compensation activities and complex...

  20. 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

  1. 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.

  2. 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...

  3. 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...

  4. O-desmethylquinine as a cyclooxygenase-2 (COX-2) inhibitors using AutoDock Vina

    Science.gov (United States)

    Damayanti, Sophi; Mahardhika, Andhika Bintang; Ibrahim, Slamet; Chong, Wei Lim; Lee, Vannajan Sanghiran; Tjahjono, Daryono Hadi

    2014-10-01

    Computational approach was employed to evaluate the biological activity of novel cyclooxygenase-2 COX-2 inhibitor, O-desmethylquinine, in comparison to quinine as common inhibitor which can also be used an agent of antipyretic, antimalaria, analgesic and antiinflamation. The molecular models of the compound were constructed and optimized with the density function theory with at the B3LYP/6-31G (d,p) level using Gaussian 09 program. Molecular docking studies of the compounds were done to obtain the COX-2 complex structures and their binding energies were analyzed using the AutoDock Vina. The results of docking of the two ligands were comparable and cannot be differentiated from the energy scoring function with AutoDock Vina.

  5. 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

  6. Identification of Potential PPAR γ Agonists as Hypoglycemic Agents: Molecular Docking Approach.

    Science.gov (United States)

    Mishra, Ganesh Prasad; Sharma, Rajesh

    2016-09-01

    Peroxisome proliferator-activated receptor gamma (PPAR γ) has become an attractive molecular target for drugs that aim to treat hyperglycemia. The object of our study is to identify the required molecular descriptor and essential amino acid residues for effective PPAR γ agonistic activity. In this work, we employed Molegro Virtual Docker program in all molecular docking simulations. Accuracy of receptor-compound docking was validated on a set of 15 PPAR γ-compound complexes for which crystallographic structures were available. The reliability of the docking results was acceptable with good root-mean-square deviation value (<2 Å). A significant correlation between different data derived from docking calculations and experimental data was revealed. Our results allowed identification of compounds with potential to become drugs against hyperglycemia. PMID:26374652

  7. 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...

  8. 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

  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. 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.

  11. Alignment of synaptic vesicle macromolecules with the macromolecules in active zone material that direct vesicle docking.

    Directory of Open Access Journals (Sweden)

    Mark L Harlow

    Full Text Available Synaptic vesicles dock at active zones on the presynaptic plasma membrane of a neuron's axon terminals as a precondition for fusing with the membrane and releasing their neurotransmitter to mediate synaptic impulse transmission. Typically, docked vesicles are next to aggregates of plasma membrane-bound macromolecules called active zone material (AZM. Electron tomography on tissue sections from fixed and stained axon terminals of active and resting frog neuromuscular junctions has led to the conclusion that undocked vesicles are directed to and held at the docking sites by the successive formation of stable connections between vesicle membrane proteins and proteins in different classes of AZM macromolecules. Using the same nanometer scale 3D imaging technology on appropriately stained frog neuromuscular junctions, we found that ∼10% of a vesicle's luminal volume is occupied by a radial assembly of elongate macromolecules attached by narrow projections, nubs, to the vesicle membrane at ∼25 sites. The assembly's chiral, bilateral shape is nearly the same vesicle to vesicle, and nubs, at their sites of connection to the vesicle membrane, are linked to macromolecules that span the membrane. For docked vesicles, the orientation of the assembly's shape relative to the AZM and the presynaptic membrane is the same vesicle to vesicle, whereas for undocked vesicles it is not. The connection sites of most nubs on the membrane of docked vesicles are paired with the connection sites of the different classes of AZM macromolecules that regulate docking, and the membrane spanning macromolecules linked to these nubs are also attached to the AZM macromolecules. We conclude that the luminal assembly of macromolecules anchors in a particular arrangement vesicle membrane macromolecules, which contain the proteins that connect the vesicles to AZM macromolecules during docking. Undocked vesicles must move in a way that aligns this arrangement with the AZM

  12. 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.

  13. Compensation following bilateral vestibular damage

    Directory of Open Access Journals (Sweden)

    Bill J Yates

    2011-12-01

    Full Text Available Bilateral loss of vestibular inputs affects far fewer patients than unilateral inner ear damage, and thus has been understudied. In both animal subjects and human patients, bilateral vestibular hypofunction (BVH produces a variety of clinical problems, including impaired balance control, inability to maintain stable blood pressure during postural changes, difficulty in visual targeting of images, and disturbances in spatial memory and navigational performance. Experiments in animals have shown that nonlabyrinthine inputs to the vestibular nuclei are rapidly amplified following the onset of BVH, which may explain the recovery of postural stability and orthostatic tolerance that occurs within 10 days. However, the loss of the vestibulo-ocular reflex and degraded spatial cognition appear to be permanent in animals with BVH. Current concepts of the compensatory mechanisms in humans with BVH are largely inferential, as there is a lack of data from patients early in the disease process. Translation of animal studies of compensation for BVH into therapeutic strategies and subsequent application in the clinic is the most likely route to improve treatment. In addition to physical therapy, two types of prosthetic devices have been proposed to treat individuals with bilateral loss of vestibular inputs: those that provide tactile stimulation to indicate body position in space, and those that deliver electrical stimuli to branches of the vestibular nerve in accordance with head movements. The relative efficacy of these two treatment paradigms, and whether they can be combined to facilitate recovery, is yet to be ascertained.

  14. 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

  15. Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls

    Directory of Open Access Journals (Sweden)

    Hezekiel Mathambo Kumalo

    2015-01-01

    Full Text Available he present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i covalent interactions in biomolecular systems; (ii the mathematical framework of covalent molecular docking; (iii implementation of covalent docking protocol in drug design workflows; (iv applications covalent docking: case studies and (v shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.

  16. A comparison of various optimization algorithms of protein-ligand docking programs by fitness accuracy.

    Science.gov (United States)

    Guo, Liyong; Yan, Zhiqiang; Zheng, Xiliang; Hu, Liang; Yang, Yongliang; Wang, Jin

    2014-07-01

    In protein-ligand docking, an optimization algorithm is used to find the best binding pose of a ligand against a protein target. This algorithm plays a vital role in determining the docking accuracy. To evaluate the relative performance of different optimization algorithms and provide guidance for real applications, we performed a comparative study on six efficient optimization algorithms, containing two evolutionary algorithm (EA)-based optimizers (LGA, DockDE) and four particle swarm optimization (PSO)-based optimizers (SODock, varCPSO, varCPSO-ls, FIPSDock), which were implemented into the protein-ligand docking program AutoDock. We unified the objective functions by applying the same scoring function, and built a new fitness accuracy as the evaluation criterion that incorporates optimization accuracy, robustness, and efficiency. The varCPSO and varCPSO-ls algorithms show high efficiency with fast convergence speed. However, their accuracy is not optimal, as they cannot reach very low energies. SODock has the highest accuracy and robustness. In addition, SODock shows good performance in efficiency when optimizing drug-like ligands with less than ten rotatable bonds. FIPSDock shows excellent robustness and is close to SODock in accuracy and efficiency. In general, the four PSO-based algorithms show superior performance than the two EA-based algorithms, especially for highly flexible ligands. Our method can be regarded as a reference for the validation of new optimization algorithms in protein-ligand docking.

  17. Connection stiffness and dynamical docking process of flux pinned spacecraft modules

    Science.gov (United States)

    Lu, Yong; Zhang, Mingliang; Gao, Dong

    2014-02-01

    This paper describes a novel kind of potential flux pinned docking system that consists of guidance navigation and control system, the traditional extrusion type propulsion system, and a flux pinned docking interface. Because of characteristics of passive stability of flux pinning, the docking control strategy of flux pinned docking system only needs a series of sequential control rather than necessary active feedback control, as well as avoidance of hazardous collision accident. The flux pinned force between YBaCuO (YBCO) high temperature superconductor bulk and permanent magnet is able to be given vent based on the identical current loop model and improved image dipole model, which can be validated experimentally. Thus, the connection stiffness between two flux pinned spacecraft modules can be calculated based on Hooke's law. This connection stiffness matrix at the equilibrium position has the positive definite performance, which can validate the passively stable connection of two flux pinned spacecraft modules theoretically. Furthermore, the relative orbital dynamical equation of two flux pinned spacecraft modules can be established based on Clohessy-Wiltshire's equations and improved image dipole model. The dynamical docking process between two flux pinned spacecraft modules can be obtained by way of numerical simulation, which suggests the feasibility of flux pinned docking system.

  18. Connection stiffness and dynamical docking process of flux pinned spacecraft modules

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Yong; Zhang, Mingliang, E-mail: niudun12@126.com; Gao, Dong [School of Mechatronics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150001 (China)

    2014-02-14

    This paper describes a novel kind of potential flux pinned docking system that consists of guidance navigation and control system, the traditional extrusion type propulsion system, and a flux pinned docking interface. Because of characteristics of passive stability of flux pinning, the docking control strategy of flux pinned docking system only needs a series of sequential control rather than necessary active feedback control, as well as avoidance of hazardous collision accident. The flux pinned force between YBaCuO (YBCO) high temperature superconductor bulk and permanent magnet is able to be given vent based on the identical current loop model and improved image dipole model, which can be validated experimentally. Thus, the connection stiffness between two flux pinned spacecraft modules can be calculated based on Hooke's law. This connection stiffness matrix at the equilibrium position has the positive definite performance, which can validate the passively stable connection of two flux pinned spacecraft modules theoretically. Furthermore, the relative orbital dynamical equation of two flux pinned spacecraft modules can be established based on Clohessy-Wiltshire's equations and improved image dipole model. The dynamical docking process between two flux pinned spacecraft modules can be obtained by way of numerical simulation, which suggests the feasibility of flux pinned docking system.

  19. 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.

  20. 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.

  1. GVD compensation schemes with considering PMD

    Institute of Scientific and Technical Information of China (English)

    Aiying Yang(杨爱英); Anshi Xu(徐安士); Deming Wu(吴德明)

    2003-01-01

    Three group velocity dispersion (GVD) compensation schemes, i.e., the post-compensation, pre-compensation and hybrid-compensation schemes, are discussed with considering polarization mode disper-sion (PMD). In the 10- and 40-Gbit/s non-return-zero (NRZ) on-off-key (OOK) systems, three physicalfactors, Kerr effect, GVD and PMD are considered. The numerical results show that, when the impactof PMD is taken into account, the GVD pre-compensation scheme performs best with more than 1 dBbetter of average eye-opening penalty (EOP) when input power is up to 10 dBm in the 10-Gbit/s system.However the GVD post-compensation scheme perforns best for the case of 40 Gbit/s with input power lessthan 13 dBm, and GVD pre-compensation will be better if the input power increased beyond this range.The results are different from those already reported under the assumption that the impact of PMD isneglected. Therefore, the research in this paper provide a different insight into the system optimizationwhen PMD, Kerr effect and GVD are considered.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. Inhibitors of polyhydroxyalkanoate (PHA) synthases: synthesis, molecular docking, and implications.

    Science.gov (United States)

    Zhang, Wei; Chen, Chao; Cao, Ruikai; Maurmann, Leila; Li, Ping

    2015-01-01

    Polyhydroxyalkanoate (PHA) synthases (PhaCs) catalyze the formation of biodegradable PHAs that are considered to be ideal alternatives to non-biodegradable synthetic plastics. However, study of PhaCs has been challenging because the rate of PHA chain elongation is much faster than that of initiation. This difficulty, along with lack of a crystal structure, has become the main hurdle to understanding and engineering PhaCs for economical PHA production. Here we report the synthesis of two carbadethia CoA analogues--sT-CH2-CoA (26 a) and sTet-CH2-CoA (26 b)--as well as sT-aldehyde (saturated trimer aldehyde, 29), as new PhaC inhibitors. Study of these analogues with PhaECAv revealed that 26 a/b and 29 are competitive and mixed inhibitors, respectively. Both the CoA moiety and extension of PHA chain will increase binding affinity; this is consistent with our docking study. Estimation of the Kic values of 26 a and 26 b predicts that a CoA analogue incorporating an octameric hydroxybutanoate (HB) chain might facilitate the formation of a kinetically well-behaved synthase.

  7. Compensator configurations for load currents' symmetrization

    Science.gov (United States)

    Rusinaru, D.; Manescu, L. G.; Dinu, R. C.

    2016-02-01

    This paper approaches aspects regarding the mitigation effects of asymmetries in 3-phase 3-wire networks. The measure consisting in connecting of load current symmetrization devices at the load coupling point is presented. A time-variation of compensators parameters is determined as a function of the time-recorded electrical values. The general sizing principle of the load current symmetrization reactive components is based on a simple equivalent model of the unbalanced 3-phase loads. By using these compensators a certain control of the power components transits is ensured in the network. The control is based on the variations laws of the compensators parameters as functions of the recorded electrical values: [B] = [T]·[M]. The link between compensator parameters and measured values is ensured by a transformation matrix [T] for each operation conditions of the supply network. Additional conditions for improving of energy and efficiency performance of the compensator are considered: i.e. reactive power compensation. The compensator sizing algorithm was implemented into a MATLAB environment software, which generate the time-evolution of the parameters of load current symmetrization device. The input data of application takes into account time-recording of the electrical values. By using the compensator sizing software, some results were achieved for the case of a consumer connected at 20 kV busbar of a distribution substation, during 24 hours measurement session. Even the sizing of the compensators aimed some additional network operation aspects (power factor correction) correlated with the total or major load symmetrizations, the harmonics aspects of the network values were neglected.

  8. Compensation for occupational diseases in the RSA.

    Science.gov (United States)

    Myers, J E; Garisch, D; Cornell, J E

    1987-03-01

    Compensation legislation for occupational disease in the RSA is at present complex and non-uniform, and the administrative bodies that process compensation claims are understaffed. In this setting occupational disease, particularly in migrant workers who are often ignorant of their rights under the law, frequently goes uncompensated. General practitioners and medical officers need to be aware of the basic provisions in the law, and how to submit claims in the best interests of their patients. Some case studies are included to illustrate problematic areas. The responsibilities of doctors in the diagnosis and compensation of occupational diseases are addressed.

  9. Advanced median method for timing jitter compensation

    Institute of Scientific and Technical Information of China (English)

    Wang Chen; Zhu Jiangmiao; Jan Verspecht; Liu Mingliang; Li Yang

    2008-01-01

    Timing jitter is one of the main factors that influence on the accuracy of time domain precision measurement. Timing jitter compensation is one of the problems people concern. Because of the flaws of median method, PDF deconvolution method and synthetic method, we put forward a new method for timing jitter compensation, which is called advanced median method. The theory of the advanced median method based on probability and statistics is analyzed, and the process of the advanced median method is summarized in this paper. Simulation and experiment show that compared with other methods, the new method could compensate timing jitter effectively.

  10. A Study on Compensation for Advertisement Translation

    Institute of Scientific and Technical Information of China (English)

    杨兰兰

    2012-01-01

    Considering the linguistic and cultural difference between English and Chinese, it is inevitable to lose the original musical beauty, visual beauty and original rhetorical devices in advertisements translation. So compensation measures are always taken to compensate the lost information. This paper focuses on the discussion of the features of advertisement, cultural and linguistic differences between English and Chinese advertisements, which result in the loss of information. And compensation strategies on words, musical beauty and rhetorical devices in advertisement translation are introduced in this paper.

  11. Lossless Compression of Video using Motion Compensation

    DEFF Research Database (Denmark)

    Martins, Bo; Forchhammer, Søren

    1998-01-01

    Summary form only given. We investigate lossless coding of video using predictive coding and motion compensation. The new coding methods combine state-of-the-art lossless techniques as JPEG (context based prediction and bias cancellation, Golomb coding), with high resolution motion field estimation...... information is coded with the same algorithm as is used for the data. For slow pan or slow zoom sequences, coding methods that use multiple previous images perform up to 20% better than motion compensation using a single previous image and up to 40% better than coding that does not utilize motion compensation...

  12. Zero energy buildings and mismatch compensation factors

    DEFF Research Database (Denmark)

    Lund, Henrik; Marszal, Anna Joanna; Heiselberg, Per

    2011-01-01

    individual buildings and an element of economy of scale. For these three reasons mismatches should be dealt with at the aggregated level and not at the individual level of each building. Instead, this paper suggests to compensate the mismatch of a building by increasing (or decreasing) the capacity...... of the energy production unit. Based on historical data for the electricity supply area in western Denmark, this paper makes a first attempt to quantify mismatch compensation factors. The results indicate that such compensation factors are a little below one for buildings with photovoltaics (PV) and a little...

  13. Lossless Compression of Video using Motion Compensation

    DEFF Research Database (Denmark)

    Martins, Bo; Forchhammer, Søren

    1998-01-01

    We investigate lossless coding of video using predictive coding andmotion compensation. The methods incorporate state-of-the-art lossless techniques such ascontext based prediction and bias cancellation, Golomb coding, high resolution motion field estimation,3d-dimensional predictors, prediction...... using one or multiple previous images, predictor dependent error modelling, and selection of motion field by code length. For slow pan or slow zoom sequences, coding methods that use multiple previous images are up to 20% better than motion compensation using a single previous image and up to 40% better...... than coding that does not utilize motion compensation....

  14. 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

  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. Comprehensive Environmental Response, Compensation and Liability Act

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), commonly known as Superfund, provides a federal "superfund" to clean up...

  17. Compensating for estimation smoothing in kriging

    Science.gov (United States)

    Olea, R.A.; Pawlowsky, Vera

    1996-01-01

    Smoothing is a characteristic inherent to all minimum mean-square-error spatial estimators such as kriging. Cross-validation can be used to detect and model such smoothing. Inversion of the model produces a new estimator-compensated kriging. A numerical comparison based on an exhaustive permeability sampling of a 4-fr2 slab of Berea Sandstone shows that the estimation surface generated by compensated kriging has properties intermediate between those generated by ordinary kriging and stochastic realizations resulting from simulated annealing and sequential Gaussian simulation. The frequency distribution is well reproduced by the compensated kriging surface, which also approximates the experimental semivariogram well - better than ordinary kriging, but not as well as stochastic realizations. Compensated kriging produces surfaces that are more accurate than stochastic realizations, but not as accurate as ordinary kriging. ?? 1996 International Association for Mathematical Geology.

  18. Multichannel Adaptive Polarization Mode Dispersion Compensation with One Compensator in Dense Wavelength Division Multiplexing Transmission Systems

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qi; CHEN Ming-hua; ZHANG Ji-yu; XIE Shi-zhong

    2007-01-01

    A simple two-section polarization mode dispersion(PMD) compensator is proposed for multichannel PMD compensation, which can compensate two or even more channels simultaneously. Because of the statistical characteristics and the frequency-dependence of PMD, for current single mode fiber with moderate PMD, the probability that all channels are severely degraded at the same time is extremely small, which makes it possible to compensate a dense wavelength division multiplexing(DWDM) transmission system with moderate PMD using this compensator. It is shown that the outage probability of a 40×43Gb/s DWDM transmission system using this compensator is decreased significantly from 3.6×10-3 to 3.6×10-5.

  19. Compensating Heterogeneous Salesforces: Some Explicit Solutions

    OpenAIRE

    Ram C. Rao

    1990-01-01

    This paper considers the question of how a sales manager should design the optimal compensation scheme for his salesforce when it consists of salespersons of varying selling skills, i.e., when the salesforce is heterogeneous. The manager's problem is to reward the salespersons based on observable, uncertain sales achieved by the salespersons. Under the assumption that both the manager and the salespersons are risk neutral, the optimal compensation scheme is derived. It consists of the manager...

  20. Job Dispersion and Compensating Wage Differentials

    OpenAIRE

    Paul Sullivan; Ted To

    2013-01-01

    The empirical literature on compensating wage differentials has a mixed history. While there have been some successes, much of this literature finds weak support for the theory of equalizing differences. We argue that it is dispersion in total job values or "job dispersion" that leads to biased compensating wage differential estimates. We begin by demonstrating how job dispersion can lead to biased hedonic estimates. Then we take a partial equilibrium on-the-job search model with utility from...

  1. Compensating fields and anomalies in supergravity

    International Nuclear Information System (INIS)

    We discuss the quantization of theories which are formulated using compensating fields. In particular, we discuss the relation between the components formulation and the superspace formulation of supergravity theories. The requirement that the compensating field can be eliminated at the quantum level gives rise to on-shell constraints on the operators of the theory. In some cases, the constraints turn out to be physically unacceptable. Using these considerations we show that new minimal supergravity is in general anomalous. (author). 17 refs

  2. Compensating Fields and Anomalies in Supergravity

    CERN Document Server

    Shamir, Y

    1993-01-01

    We discuss the quantization of theories which are formulated using compensating fields. In particular, we discuss the relation between the components formulation and the superspace formulation of supergravity theories. The requirement that the compensating field can be eliminated at the quantum level gives rise to on-shell constraints on the operators of the theory. In some cases, the constraints turn out to be physically unacceptable. Using these considerations we show that new minimal supergravity is in general anomalous.

  3. Stock Option Compensation and Managerial Turnover

    OpenAIRE

    Raluca Georgiana NASTASESCU

    2009-01-01

    This study examines the association between managerial turnover and equity-based compensation. I investigate whether stock options act to bond executives to their firms and whether retention of managers is a motivation of companies in designing CEO incentive contracts. The results show that stock options do negatively influence the probability of a CEO leaving the company. The monetary cost of losing the value of equity-based compensation package keeps the manager with his company. I also fin...

  4. Nonlinear Thermal Compensators for WGM Resonators

    Science.gov (United States)

    Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry; Maleki, Lute; Yu, Nan; Iltchenko, Vladimir

    2009-01-01

    In an alternative version of a proposed bimaterial thermal compensator for a whispering-gallery-mode (WGM) optical resonator, a mechanical element having nonlinear stiffness would be added to enable stabilization of a desired resonance frequency at a suitable fixed working temperature. The previous version was described in "Bimaterial Thermal Compensators for WGM Resonators." Both versions are intended to serve as inexpensive means of preventing (to first order) or reducing temperature-related changes in resonance frequencies.

  5. Improved charge amplifier using hybrid hysteresis compensation

    Science.gov (United States)

    Amin-Shahidi, Darya; Trumper, David L.

    2013-08-01

    We present a novel charge amplifier, with a robust feedback circuit and a method for compensating piezoelectric actuator's hysteresis at low frequencies. The amplifier uses a modified feedback circuit which improves robustness to the addition of series load impedance such as in cabling. We also describe a hybrid hysteresis compensation method for enabling the charge amplifier to reduce hysteresis at low frequencies. Experimental results demonstrate the utility of the new amplifier design.

  6. Empirical Evidence of Recurring International Compensation Problems

    OpenAIRE

    Michael Harvey

    1993-01-01

    The expansion of international business necessitates an increased number of employees based in foreign markets. These expatriates, nationals and third-country nationals represent unique and complex compensation problems. This article addresses five of the recurring compensation problems reported by members of the Society for Human Resource Management International (SHRMI) in a recent survey.© 1993 JIBS. Journal of International Business Studies (1993) 24, 785–799

  7. Reactive power compensation a practical guide

    CERN Document Server

    Hofmann, Wolfgang; Just, Wolfgang

    2012-01-01

    The comprehensive resource on reactive power compensation, presenting the design, application and operation of reactive power equipment and installations The area of reactive power compensation is gaining increasing importance worldwide. If suitably designed, it is capable of improving voltage quality significantly, meaning that losses in equipment and power systems are reduced, the permissible loading of equipment can be increased, and the over-all stability of system operation improved. Ultimately, energy use and CO2 emisson are reduced. This unique guide discusses the

  8. Temperature-Compensating Inactive Strain Gauge

    Science.gov (United States)

    Moore, Thomas C., Sr.

    1993-01-01

    Thermal contribution to output of active gauge canceled. High-temperature strain gauges include both active gauge wires sensing strains and inactive gauge wires providing compensation for thermal contributions to gauge readings. Inactive-gauge approach to temperature compensation applicable to commercially available resistance-type strain gauges operating at temperatures up to 700 degrees F and to developmental strain gauges operating at temperatures up to 2,000 degrees F.

  9. Managing workers' compensation exposures in healthcare.

    Science.gov (United States)

    McDonald, L

    1998-01-01

    Employees in healthcare are exposed to numerous and varied risks that pose the threat of injury. Management of those exposures by the organization will ultimately help create a safe environment for staff, patients and the public. Incorporating workers' compensation into the risk management program is the first step toward managing and reducing these exposures. This article presents a suggested outline for a written risk management plan for workers' compensation exposures. PMID:10182134

  10. Increasing of AC compensation method accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Havlicek, V. E-mail: havlicek@fel.cvut.cz; Pokorny, M

    2003-01-01

    The original MMF compensation method allows the magnetic properties of single sheets and strips to be measured in the same way as the closed specimen properties. The accuracy of the method is limited due to the finite gain of the feedback loop fulfilling the condition of its stability. Digitalisation of the compensation loop appropriate processing of the error signal can rapidly improve the accuracy. The basic ideas of this new approach and the experimental results are described in this paper.

  11. Reversible thyristor converters of brushless synchronous compensators

    Directory of Open Access Journals (Sweden)

    А.М.Galynovskiy

    2013-12-01

    Full Text Available Behavior of models of three-phase-to-single-phase rotary reversible thyristor converters of brushless synchronous compensators in a circuit simulation system is analyzed. It is shown that combined control mode of opposite-connected thyristors may result in the exciter armature winding short circuits both at the thyristor feed-forward and lagging current delay angles. It must be taken into consideration when developing brushless compensator excitation systems.

  12. Compensation and Incentives in German Corporations

    OpenAIRE

    Moritz Heimes; Steffen Seemann

    2011-01-01

    In this paper we analyze executive compensation in Germany for the period 2005-2009. We use a self-collected dataset on compensation arrangements in German corporations to estimate the impact of firm performance and firm risk on executive pay. To be in line with earlier studies in this literature, we first measure firm performance and firm risk based on stock market returns. Our findings support the prediction from agency theory that incentive pay decreases with firm risk. We find, however, t...

  13. Executive equity compensation and incentives: a survey

    OpenAIRE

    Core, John E.; Wayne R. Guay; David F. Larcker

    2003-01-01

    Stock and option compensation and the level of managerial equity incentives are aspects of corporate governance that are especially controversial to shareholders, institutional activists, and government regulators. Similar to much of the corporate finance and corporate governance literature, research on stock-based compensation and incentives has not only generated useful insights, but also produced many contradictory findings. Not surprisingly, many fundamental questions remain unanswered. I...

  14. A compensation index for multiattribute decision strategies.

    Science.gov (United States)

    Koele, P; Westenberg, M R

    1995-09-01

    In multiattribute decision problems, the subject has to evaluate a number of alternatives with given values on a number of attributes, in order to arrive at some conclusion about the attractiveness or utility of these alternatives. The information processing procedure leading to a conclusion is called adecision strategy, and one of the main research topics in multiattribute decision research has been the extent to which these strategies follow compensatory principles. Judges are said to follow compensatory strategies when low values on some attributes are compensated for by high values on other attributes. In process tracing studies using the information board technique, descriptions of decision strategies are usually based on three indices of the information search process:variability of search,search pattern (Payne, 1976), anddepth of search. Variability of search, defined as the standard deviation of the proportion of information searched per alternative, is considered to give an indication of the degree of compensation of a decision strategy, compensation being smaller as variability increases. In this article, we propose an alternative way for establishing the degree of compensation of decision strategies in information board studies. We argue that the degree of compensation depends on both variability of searchand depth of search (the proportion of information searched), and that a valid compensation index has to be a multiplicative function of these two indices.

  15. Overcoming maladaptive plasticity through plastic compensation

    Institute of Scientific and Technical Information of China (English)

    Matthew R.J.MORRIS; Sean M.ROGERS

    2013-01-01

    Most species evolve within fluctuating environments,and have developed adaptations to meet the challenges posed by environmental heterogeneity.One such adaptation is phenotypic plasticity,or the ability of a single genotype to produce multiple environmentally-induced phenotypes.Yet,not all plasticity is adaptive.Despite the renewed interest in adaptive phenotypic plasticity and its consequences for evolution,much less is known about maladaptive plasticity.However,maladaptive plasticity is likely an important driver of phenotypic similarity among populations living in different environments.This paper traces four strategies for overcoming maladaptive plasticity that result in phenotypic similarity,two of which involve genetic changes (standing genetic variation,genetic compensation) and two of which do not (standing epigenetic variation,plastic compensation).Plastic compensation is defined as adaptive plasticity overcoming maladaptive plasticity.In particular,plastic compensation may increase the likelihood of genetic compensation by facilitating population persistence.We provide key terms to disentangle these aspects of phenotypic plasticity and introduce examples to reinforce the potential importance of plastic compensation for understanding evolutionary change.

  16. Statutory Compensation for the Wrongly Imprisoned.

    Science.gov (United States)

    Simms, Tina

    2016-04-01

    This article provides an overview of the unique challenges faced by men and women who have been wrongly convicted, imprisoned, and subsequently exonerated, and discusses the relevance of social work to exoneration. The ways in which exonerees can seek compensation are described, and state compensation statutes are examined, delineating monetary and reentry support provisions. Currently, 30 states and the District of Columbia have compensation statutes. Monetary and reentry support provisions vary greatly by state, with few providing both. The wrongly imprisoned experience the same effects of incarceration as other prisoners; their psychological trauma, however, is exacerbated by the fact that they are innocent. Furthermore, upon release, exonerees have fewer reentry supports available to them compared with prisoners released on parole. This article supports the position that the state has a responsibility to provide adequate compensation, monetarily and servicewise, to the wrongly imprisoned, and that compensation by statutory means should be standard in every state. This article also highlights how social workers are uniquely qualified to provide immediate and long-term social and mental health services to exonerees, as well as to advocate for comprehensive exoneree compensation through state statutes.

  17. 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.

  18. 31 CFR 30.0 - Executive compensation and corporate governance.

    Science.gov (United States)

    2010-07-01

    ... STANDARDS FOR COMPENSATION AND CORPORATE GOVERNANCE § 30.0 Executive compensation and corporate governance. The following questions and answers reflect the executive compensation and corporate governance... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Executive compensation and...

  19. 20 CFR 226.63 - Determining monthly compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Determining monthly compensation. 226.63... COMPUTING EMPLOYEE, SPOUSE, AND DIVORCED SPOUSE ANNUITIES Years of Service and Average Monthly Compensation § 226.63 Determining monthly compensation. (a) Based on yearly compensation. If Board records do...

  20. 20 CFR 336.4 - Base year compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Base year compensation. 336.4 Section 336.4... DURATION OF NORMAL AND EXTENDED BENEFITS Normal Benefits § 336.4 Base year compensation. (a) Formula. For the purposes of this part, an employee's base year compensation includes any compensation in excess...

  1. 46 CFR 535.803 - Ocean freight forwarder compensation.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 9 2010-10-01 2010-10-01 false Ocean freight forwarder compensation. 535.803 Section... Mandatory and Prohibited Provisions § 535.803 Ocean freight forwarder compensation. No conference or group... compensation paid to an ocean freight forwarder; or (b) Agree to limit the payment of compensation to an...

  2. 50 CFR 296.4 - Claims eligible for compensation.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Claims eligible for compensation. 296.4... compensation. (a) Claimants. Damage or loss eligible for Fund compensation must be suffered by a commercial fisherman. (b) Damage or loss of fishing gear. Damage or loss is eligible for Fund compensation if it...

  3. 47 CFR 64.1310 - Payphone compensation procedures.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 3 2010-10-01 2010-10-01 false Payphone compensation procedures. 64.1310... compensation procedures. (a) Unless the payphone service provider consents to an alternative compensation... not unreasonably withhold its consent to an alternative compensation arrangement. (1) Each...

  4. 46 CFR 2.01-60 - Overtime compensation.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Overtime compensation. 2.01-60 Section 2.01-60 Shipping... Inspecting and Certificating of Vessels § 2.01-60 Overtime compensation. (a) General. Extra compensations for... method of computing such extra compensation. (b) Application and certification of time. Application...

  5. 48 CFR 852.236-86 - Workers' compensation.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Workers' compensation. 852... Workers' compensation. As prescribed in 836.577, insert the following clause: Workers' Compensation (JAN... workers compensation laws to all lands and premises owned or held by the United States. (End of clause)...

  6. 39 CFR 3.2 - Compensation of Board.

    Science.gov (United States)

    2010-07-01

    ... 39 Postal Service 1 2010-07-01 2010-07-01 false Compensation of Board. 3.2 Section 3.2 Postal... (ARTICLE III) § 3.2 Compensation of Board. Section 202(a)(1) of title 39 provides for the compensation of... meetings. Compensation is provided for not more than 42 days of meetings per year....

  7. 20 CFR 211.5 - Employee representative compensation.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Employee representative compensation. 211.5... CREDITABLE RAILROAD COMPENSATION § 211.5 Employee representative compensation. All payments made by a railway... office he occupies with such organization are creditable as compensation, including payments made...

  8. Full structure building and docking of NifS from extremophile Acidithiobacillus ferrooxidans

    Institute of Scientific and Technical Information of China (English)

    LIU Yuan-dong; QIU Guan-zhou; WANG Hai-dong; JIANG Ying; ZHANG Cheng-gui; XIA Le-xia

    2008-01-01

    The gene iscS-2 from extremophile Acidithiobacillus ferrooxidans may play a crucial role in nitrogenase maturation. To investigate the protein encoded by this gene, a reliable integral three-dimensional molecular structure was built. The obtained structure was further used to search binding sites, carry out the flexible docking with cofactor pyridoxal 5′-phosphate(PLP) and substrate cysteine, and identify its key residues. The docking results of PLP reveal that the residues of Lys203, His100, Thr73, Ser200, His202, Asp177 and Gln180 have large interaction energies and/or hydrogen bonds fixation with PLP. The docking results of cysteine show that the amino group in cysteine is very near His100, Lys203 and PLP, and the interaction energies for cysteine with them are very big. These identified residues are in line with the experimental facts of NifS from other sources. Moreover, the four residues of Asn152, Val179, Ala102 and Met148 in the PLP docking and the two residues of Lys208 and Ala102 in the cysteine docking also have large interaction energies, which are fitly conserved in NifS from all kinds of sources but have not been identified before. According to these results, this gene encodes NifS protein, and the substrate cysteine can be effectively recruited into the active site. Furthermore, all of the above detected key residues are directly responsible for the binding and/or catalysis of PLP and cysteine.

  9. Structural determinants of resveratrol for cell proliferation inhibition potency: experimental and docking studies of new analogs.

    Science.gov (United States)

    Mazué, Frédéric; Colin, Didier; Gobbo, Jessica; Wegner, Maria; Rescifina, Antonio; Spatafora, Carmela; Fasseur, Dominique; Delmas, Dominique; Meunier, Philippe; Tringali, Corrado; Latruffe, Norbert

    2010-07-01

    Resveratrol is the subject of intense research because of the abundance of this compound in the human diet and as one of the most valuable natural chemopreventive agents. Further advances require new resveratrol analogs be used to identify the structural determinants of resveratrol for the inhibition potency of cell proliferation by comparing experimental and docking studies. Therefore, we synthesized new trans/(E)- and cis/(Z)-resveratrol - analogs not reported to date - by modifying the hydroxylation pattern of resveratrol and a double bond geometry. We included them in a larger panel of 14 molecules, including (Z)-3,5,4'-trimethoxystilbene, the most powerful molecule that is used as reference. Using a docking model complementary to experimental studies on the proliferation inhibition of the human colorectal tumor SW480 cell line, we show that methylation is the determinant substitution in inhibition efficacy, but only in molecules bearing a Z configuration. Most of the synthetic methylated derivatives (E or Z) stop mitosis at the M phase and lead to polyploid cells, while (E)-resveratrol inhibits cells at the S phase. Docking studies show that almost all of the docked structures of (Z)-polymethoxy isomers, but not most of the (E)-polymethoxy isomers substantially overlap the docked structure of combretastatin A-4, taken as reference ligand at the colchicine-tubulin binding site. PMID:20395019

  10. DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith

    2014-01-01

    Full Text Available We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc., a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

  11. The relationship between tail biting in pigs, docking procedure and other management practices.

    Science.gov (United States)

    Hunter, E J; Jones, T A; Guise, H J; Penny, R H; Hoste, S

    2001-01-01

    The tail length (docked, tipped or undocked) and tail status (bitten or unbitten) of 27,870 pigs from 450 units was recorded at six UK abattoirs. A farm survey of the final finishing stage was used to investigate the relationship between management practice and tail biting. This showed that docking was the most important factor influencing the probability of being not bitten, with 2.4% of docked and 8.5% of long-tailed pigs being tail-bitten. The following factors reduced the probability of long-tailed pigs being tail-bitten; light straw provision, use of natural ventilation or artificially controlled natural ventilation (ACNV), mixed sex grouping, meal or liquid feeding, and use of double or multi-space feeders. Docked and long-tailed pigs provided with light straw and natural ventilation/ACNV had levels of tail biting of 1.2% and 4.3% respectively; 3.9% of docked pigs with artificial ventilation and no straw were tail-bitten. Long-tailed pigs fed via double or multi-space feeders also had 3.9% of tails bitten. PMID:11145831

  12. 38 CFR 21.3023 - Nonduplication; pension, compensation, and dependency and indemnity compensation.

    Science.gov (United States)

    2010-07-01

    ... parents. Where, however, entitlement is based on the death of more than one parent in the same parental... before attaining age 18 or while helpless based on the service of another parent in the same parental... concurrently with pension, compensation or dependency and indemnity compensation. (Authority: 38 U.S.C....

  13. Do executives get appropriate compensation? : Evidence from intellectual capital perspective

    OpenAIRE

    Xie, Yamin

    2013-01-01

    This paper presents an empirical analysis of top executive compensation from intellectual capital perspective using data from US listed companies and aims to examine whether executives get appropriate compensation. I propose a pay-contribution compensation scheme and extend previous research on agency theory, by exploring how executive compensation contract design may be based on the firm’s intellectual capital (IC). Such features would serve the core purpose of compensation design, which is ...

  14. An Economic Analysis of Compensation for Rural Land Expropriation

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    To study which method is more effective in complete compensation and zero compensation for rural land expropriation,we use economic models to analyze whether the government is benevolent and which compensation method can achieve the social optimal level.The results show that both complete compensation and zero compensation will lead to over-investment of land owners,and consequently result in loss of social welfare.

  15. Managerial Stock Compensation and Risky Investment

    Directory of Open Access Journals (Sweden)

    Raluca Georgiana Nastasescu

    2009-06-01

    Full Text Available This study analyzes the relationship between the mix of CEO equity-based compensation, namely stock options and restricted stock, and firms' risky investment. In general, the theory suggests that long-term compensation aligns CEOs' and shareholders' interests by inducing the managers to undertake risky investment, which has a positive impact on longterm well-being of the firm. However, as my results show, it is important to distinguish between types of awards since they can have different effects on the riskiness of the firm. In this respect, I answer the question how are different types of stock based compensation related to the executives' determination to increase or not the intensity of the firm's risky investment? I find that awarding the CEOs preponderantly with stock options positively affects the firm's level of R&D investment. Conversely, a higher proportion of restricted stock in the CEO's compensation is related to lower investment in (risky R&D. The inverse relation of causality also holds. Firms that make intensive R&D investments are more likely to award their CEOs with more stock options relative to restricted stock. Overall, the results are consistent with the theoretical prediction, in that the managerial compensation scheme plays an important role in determining the level of R&D investment.

  16. Risk compensation behaviours in construction workers' activities.

    Science.gov (United States)

    Feng, Yingbin; Wu, Peng

    2015-01-01

    The purpose of this study was to test whether the construction workers have the tendency of engaging in risk compensation behaviours, and identify the demographic variables, which may influence the extent to which the construction workers may show risk compensation behaviours. Both quantitative (survey) and qualitative (interviews) approaches were used in this study. A questionnaire survey was conducted with all the construction workers on three building construction sites of a leading construction company in Australia. Semi-structured interviews were then conducted to validate the findings of the quantitative research. The findings indicate that workers tend to show risk compensation behaviours in the construction environment. The workers with more working experience, higher education, or having never been injured at work before have a higher tendency to show risk compensation in their activities than the others. The implication is that contractors need to assess the potential influence of workers' risk compensation behaviours when evaluating the effect of risk control measures. It is recommended that supervisors pay more attention to the behavioural changes of those workers who have more experience, higher education, and have never been injured before after the implementation of new safety control measures on construction site. PMID:24134314

  17. Comparative docking and CoMFA analysis of curcumine derivatives as HIV-1 integrase inhibitors.

    Science.gov (United States)

    Gupta, Pawan; Garg, Prabha; Roy, Nilanjan

    2011-08-01

    The docking studies and comparative molecular field analysis (CoMFA) were performed on highly active molecules of curcumine derivatives against 3' processing activity of HIV-1 integrase (IN) enzyme. The optimum CoMFA model was selected with statistically significant cross-validated r(2) value of 0.815 and non-cross validated r (2) value of 0.99. The common pharmacophore of highly active molecules was used for screening of HIV-1 IN inhibitors. The high contribution of polar interactions in pharmacophore mapping is well supported by docking and CoMFA results. The results of docking, CoMFA, and pharmacophore mapping give structural insights as well as important binding features of curcumine derivatives as HIV-1 IN inhibitors which can provide guidance for the rational design of novel HIV-1 IN inhibitors. PMID:21327540

  18. Modulation of current through a nanopore induced by a charged globule: implications for DNA-docking

    CERN Document Server

    Chinappi, Mauro; Cecconi, Fabio; Marconi, Umberto Marini Bettolo; Melchionna, Simone

    2015-01-01

    The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of the two events. However, at low voltages a clear distinction of the two phases is lost. By using numerical simulations we clarify how the current signature associated to the docking events depends on the applied voltage. The simulations show that at small voltage the DNA globule enhances the pore conductance due to an enrichment of charge carriers. At high voltage, the globule drains substantial charge carriers from the pore region, thereby reducing the overall conductance. The results provide a new interpretation to the experimental data on conductance and show how docking interferes with the translocation signal, of potential interest for sequencing applications.

  19. Exploration of the binding mode between (-)-zampanolide and tubulin using docking and molecular dynamics simulation.

    Science.gov (United States)

    Liao, Si-Yan; Mo, Guang-Quan; Chen, Jin-Can; Zheng, Kang-Cheng

    2014-02-01

    The binding mode of (-)-zampanolide (ZMP) to tubulin was investigated using docking, molecular dynamics (MD) simulation, and binding free-energy calculations. The docking studies validated the experimental results indicating that the paclitaxel site is the binding site for (-)-ZMP. The 18 ns MD simulation shows the docking mode has changed a lot, whereas it offers more reliable binding data. MM-PBSA binding free-energy calculations further confirmed the results of the MD simulation. The study revealed that hydrophobic interactions play an important role in stabilizing the binding, and the strong hydrogen bond formed with Asp224 enhances the affinity for tubulin. Meanwhile, the results support the assumption that (-)-ZMP can be attacked by His227, leading to a nucleophilic reaction and covalent binding. These theoretical results lead to a greater understanding of the mechanism of action of binding to tubulin, and will therefore aid the design of new compounds with higher affinities for tubulin. PMID:24478043

  20. Synthesis of hydrazine based novel HMG coA inhibitor and its docking studies

    Directory of Open Access Journals (Sweden)

    Saravanan. B

    2013-12-01

    Full Text Available Heart attack is the recent attention to the medical sciences and cardiac low density cholesterol (LDL has a significant role in inhibiting the arrest. Various pathways having the keypoints which can interrupt the synthesis of bad cholesterol. In this study Hydrazine based compound is choosen due to its wide applications, the 1,2-Bis (2-hydroxy-5-methylbenzylidene - hydrazine crystals were synthesized. It was taken as a ligand for molecular docking. The target receptor used for docking is HMG-CoA reductase whose crystal structure is available on the PDB database as PDB ID: 1DQ8. For docking analysis, Autodock tool v4. 2 program used. The synthesized crystals are subjected to single crystal X-ray studies in order to investigate their molecular structure.

  1. What in silico molecular docking can do for the `bench-working biologists'

    Indian Academy of Sciences (India)

    Marius Mihăşan

    2012-12-01

    Required by an increasing amount of scientists, the in silico docking field is in full expansion, new algorithms and methods appearing at an exponential rate. The sheer range of available programs is overwhelming for the bench-working biologist, which is often discouraging by the lack of a graphical user interface, good user manual or literature to validate a given program. This mini-review attempts to present the docking problem and available solutions from a non-bioinformatician point of view and makes a selection of the available servers and programs. These tools are evaluated from several points of view, as numbers of citations, ease of usage and computer requirements. Finally, the capabilities and limitations as well as specific applications of in silico docking techniques are presented.

  2. Discovery of Anti-SARS Coronavirus Drug Based on Molecular Docking and Database Screening

    Institute of Scientific and Technical Information of China (English)

    CHEN,Hai-Feng(陈海峰); YAO,Jian-Hua(姚建华); SUN,Jing(孙晶); LI,Qiang(李强); LI,Feng(李丰); FAN,Bo-Tao(范波涛); YUAN,Shen-Gang(袁身刚)

    2004-01-01

    The active site of 3CL proteinase (3CLpro) for coronavirus was identified by comparing the crystal structures of human and porcine coronavirus. The inhibitor of the main protein of rhinovirus (Ag7088) could bind with 3CLpro of human coronavirus, then it was selected as the reference for molecular docking and database screening. The ligands from two databases were used to search potential lead structures with molecular docking. Several structures from natural products and ACD-SC databases were found to have lower binding free energy with 3CLpro than that of Ag7088. These structures have similar hydrophobicity to Ag7088. They have complementary electrostatic potential and hydrogen bond acceptor and donor with 3CLpro, showing that the strategy of anti-SARS drug design based on molecular docking and database screening is feasible.

  3. 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.

  4. Molecular Docking Evaluation of Imidazole Analogues as Potent Candida albicans 14α-Demethylase Inhibitors.

    Science.gov (United States)

    Rani, Nidhi; Kumar, Praveen; Singh, Randhir; Sharma, Ajay

    2015-01-01

    Candida albicans is one of the most important causes of life-threating fungal infections. Lanosterol 14α-demethylase (Cytochrome P450DM) is the target enzyme of azole antifungal agents. The study involved selection and modeling of the target enzyme followed by refinement of the model using molecular dynamic simulation. The modeled structure of enzyme was validated using Ramachandran plot and Sequence determination technique. A series of chlorosubstituted imidazole analogues were evaluated for Cytochrome P450 inhibitory activity using molecular docking studies. The imidazole analogues were prepared using Chem sketch and molecular docking was performed using Molergo Virtual Docker program. The docking study indicated that all the imidazole analogues (AN1-AN45) and standard drugs i.e., Ketoconazole, Clotrimazole and Miconazole have interaction with protein residue of 14α-demethylase, Heme cofactor and the water molecules present in the active site. PMID:26081558

  5. Development of Algorithms for Approaching and Docking Underwater Vehicle with Underwater Station

    Directory of Open Access Journals (Sweden)

    Gurenko B.V.

    2015-01-01

    Full Text Available Underwater vehicles (UV are widely spread nowadays. Their efficient application requires accompanying base ships or net of stations for technical servicing. Fast and energy-efficient docking is one of the key requirements for trouble-free operation. In this paper authors describe the research and development of algorithms for UV control system that allows docking with underwater station. The process is divided in two steps: moving to docking zone and vehicle positioning of station. First task includes development of path regulator. The proposed one features separation of control channels for simple adjustment and gives best results when multicoupling influence is low. Second task was solved on the basis of UV mathematical model. Developed control values were tested in simulation and proved themselves to be efficient. Authors give results of coordinate changes, control force modifications and deviation of velocity and orientation angles from the required values.

  6. INSILICO MODELING AND DOCKING STUDIES OF NEW DELHI METALLO BETA LACTAMASE-1 (SUPER BUG

    Directory of Open Access Journals (Sweden)

    DR. JAYASREE GANUGAPATI,

    2011-03-01

    Full Text Available New Delhi Metallo Beta Lactamase-1 (NDM-1 is a novel beta -lactamase enzyme that is ubiquitously found in Escherichia coli. This enzyme belongs to a B1 subclass of Metallo Beta Lactamases and is known to induce resistance to standard intravenous antibiotics. The tertiary structure of NDM-1 was predicted using Modeller9v7, based on the structural homology of the x-ray crystallographic structures of VIM-2 & VIM- 4 (Verona imipenemase-2 & -4 proteins from Pseudomonas aeruginosa. Further refinement of the structure was done using the loop modeling. Docking Analysis of NDM-1 with flavonoids was then performed using, GOLD, Auto Dock and Argus Lab. The analysis of the results of all three docking softwares suggested that Quercetin may be a potential inhibitor of NDM-1. Further analysis in the wet labmay provide us more information regarding inhibiting of NDM-1.

  7. 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

  8. Bimaterial Thermal Compensators for WGM Resonators

    Science.gov (United States)

    Savchenkov, Anatoliy; Yu, Nan; Maleki, Lute; Iltchenko, Vladimir; Strekalov, Dmitry

    2008-01-01

    Bimaterial thermal compensators have been proposed as inexpensive means of preventing (to first order) or reducing temperature-related changes in the resonance frequencies of whispering-gallery-mode (WGM) optical resonators. A bimaterial compensator would apply, to a WGM resonator, a pressure that would slightly change the shape of the resonator and thereby change its resonance frequencies. Through suitable choice of the compensator dimensions and materials, it should be possible to make the temperature dependence of the pressure-induced frequency shift equal in magnitude and opposite in sign to the temperature dependence of the frequency shift of the uncompensated resonator so that, to first order, a change in temperature would cause zero net change in frequency.

  9. Automatic Transaction Compensation for Reliable Grid Applications

    Institute of Scientific and Technical Information of China (English)

    Fei-Long Tang; Ming-Lu Li; Joshua Zhexue Huang

    2006-01-01

    As grid technology is expanding from scientific computing to business applications, service oriented grid computing is aimed at providing reliable services for users and hiding complexity of service processes from them. The grid services for coordinating long-lived transactions that occur in business applications play an important role in reliable grid applications. In this paper, the grid transaction service (GridTS) is proposed for dealing with long-lived business transactions. We present a compensation-based long-lived transaction coordination algorithm that enables users to select results from committed sub-transactions. Unlike other long-lived transaction models that require application programmers to develop corresponding compensating transactions, GridTS can automatically generate compensating transactions on execution of a long-lived grid transaction. The simulation result has demonstrated the feasibility of GridTS and effectiveness of the corresponding algorithm.

  10. Incomplete and imperfect information for sales compensation

    Directory of Open Access Journals (Sweden)

    Raluca Valeanu

    2010-12-01

    Full Text Available Sales force compensation represents the fix and / or variable payment by the company. To compensate agents based on the results, the company set a goal which is brought to their attention through the compensation plan. Applying the model of moral hazard, where the agent behavior cannot be verified, it cannot be specified in the contract what is the expected behavior of the agent. In order to make an offer to contract principal should know the effort that the agent will submit it to define the payment and the contract is determined optimally in trade between the two conflicting objectives of the two participants in the contract. Although agent behavior cannot be verified, the result of this behavior should be measurable at the end of the contract so that the employer may make the contract contingent on effort commission agent for sale of which is measured by the amount of earnings to the company.

  11. Supersymmetric composite gauge fields with compensators

    Science.gov (United States)

    Nishino, Hitoshi; Rajpoot, Subhash

    2016-06-01

    We study supersymmetric composite gauge theory, supplemented with compensator mechanism. As our first example, we give the formulation of N = 1 supersymmetric non-Abelian composite gauge theory without the kinetic term of a non-Abelian gauge field. The important ingredient is the Proca-Stueckelberg-type compensator scalar field that makes the gauge-boson field equation non-singular, i.e., the field equation can be solved for the gauge field algebraically as a perturbative expansion. As our second example, we perform the gauging of chiral-symmetry for N = 1 supersymmetry in four dimensions by a composite gauge field. These results provide supporting evidence for the consistency of the mechanism that combines the composite gauge field formulations and compensator formulations, all unified under supersymmetry.

  12. Compensation: Will it provide a waste site?

    International Nuclear Information System (INIS)

    Offering an attractive compensation package to persuade a community to voluntarily accept an otherwise undesirable facility may work in some cases, but it's not likely to work for high-level nuclear-waste disposal. The public perception of the risks involved and the public distrust of the institutions responsible for managing those risks are just too great. Much of the controversy stems from public perceptions that the site-selection process itself is unfair. Resentment builds when this occurs, and offers of compensation come to be labeled bribes or blood money. The driving force behind current nuclear-waste policy is intergenerational equity - the moral concept that the generation that produced the waste should dispose of it, permanently. Regardless of the moral appeal, doubts have been raised about the technical feasibility of this approach. Alternatives featuring intergenerational monetary compensation may better honor the commitment hor-ellipsis and reduce pressure to try to do what may be impossible

  13. Synthesis, anti-inflammatory evaluation and docking studies of some new fluorinated fused quinazolines.

    Science.gov (United States)

    Balakumar, C; Lamba, P; Kishore, D Pran; Narayana, B Lakshmi; Rao, K Venkat; Rajwinder, K; Rao, A Raghuram; Shireesha, B; Narsaiah, B

    2010-11-01

    A series of novel 8/10-trifluoromethyl-substituted-imidazo[1,2-c] quinazolines have been synthesized and evaluated in vivo (rat paw edema) for their anti-inflammatory activity and in silico (docking studies) to recognize the hypothetical binding motif of the title compounds with the cyclooxygenase isoenzymes (COX-1 and COX-2) employing GOLD (CCDC, 4.0.1 version) software. The compounds, 9b and 10b, were found to have good anti-inflammatory activity [around 80% of the standard: indomethacin]. The binding mode of the title compounds has been proposed based on the docking studies.

  14. Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

    Directory of Open Access Journals (Sweden)

    Chantal Prévost

    2011-02-01

    Full Text Available Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA.We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  15. Accounting for large amplitude protein deformation during in silico macromolecular docking.

    Science.gov (United States)

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-02-22

    Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  16. 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...

  17. Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

    DEFF Research Database (Denmark)

    Nguyen, E.D.; Meiler, J.; Norn, C.;

    2013-01-01

    and side-chain conformational space with Rosetta can be leveraged to meet this challenge. This study performs unbiased comparative modeling and docking methodologies using 14 distinct high-resolution GPCRs and proposes knowledge-based filtering methods for improvement of sampling performance...... extracellular loop. Furthermore, these models are consistently correlated with low Rosetta energy score. To predict their binding modes, ligand conformers of the 14 ligands co-crystalized with the GPCRs were docked against the top ranked comparative models. In contrast to the comparative models themselves...

  18. 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

  19. Synthesis, anti-inflammatory evaluation and docking studies of some new fluorinated fused quinazolines.

    Science.gov (United States)

    Balakumar, C; Lamba, P; Kishore, D Pran; Narayana, B Lakshmi; Rao, K Venkat; Rajwinder, K; Rao, A Raghuram; Shireesha, B; Narsaiah, B

    2010-11-01

    A series of novel 8/10-trifluoromethyl-substituted-imidazo[1,2-c] quinazolines have been synthesized and evaluated in vivo (rat paw edema) for their anti-inflammatory activity and in silico (docking studies) to recognize the hypothetical binding motif of the title compounds with the cyclooxygenase isoenzymes (COX-1 and COX-2) employing GOLD (CCDC, 4.0.1 version) software. The compounds, 9b and 10b, were found to have good anti-inflammatory activity [around 80% of the standard: indomethacin]. The binding mode of the title compounds has been proposed based on the docking studies. PMID:20800934

  20. Reactive Power Compensation using a Matrix Converter

    OpenAIRE

    Holtsmark, Nathalie Marie-Anna

    2010-01-01

    This Master's thesis investigates a new application for the matrix converter: Shunt reactive power compensation. The suggested Matrix Converter-based Reactive power Compensation (MCRC) device is composed of a matrix converter, which input is connected to the grid and an electric machine at the output of the converter. The reactive power flowing in or out of the grid can be regulated with the matrix converter by controlling the magnitude and/or phase angle of the current at the input of the co...

  1. Security careers skills, compensation, and career paths

    CERN Document Server

    Walker, Stephen W

    2014-01-01

    The third edition of Security Careers is the authoritative reference for current job descriptions and pay practices of security, compliance, ethics, environmental, health and safety occupations. The job descriptions and compensation ranges in this report are drawn from research from the Foushée Group, which has been conducting this research since 1980. Security Careers includes more than 75 job descriptions for security-related positions, which range from the entry-level security guard to the top global corporate executive. It also provides four years of compensation trend data to give a th

  2. Static compensators (STATCOMs) in power systems

    CERN Document Server

    Shahnia, Farhad; Ghosh, Arindam

    2014-01-01

    A static compensator (STATCOM), also known as static synchronous compensator, is a member of the flexible alternating current transmission system (FACTS) devices. It is a power-electronics based regulating device which is composed of a voltage source converter (VSC) and is shunt-connected to alternating current electricity transmission and distribution networks. The voltage source is created from a DC capacitor and the STATCOM can exchange reactive power with the network. It can also supply some active power to the network, if a DC source of power is connected across the capacitor. A STATCOM

  3. Filament stretching rheometer: inertia compensation revisited

    DEFF Research Database (Denmark)

    Szabo, Peter; McKinley, Gareth H.

    2003-01-01

    The necessary inertia compensation used in the force balance for the filament stretching rheometer is derived for an arbitrary frame of reference. This enables the force balance to be used to extract correctly the extensional viscosity from measurements of the tensile force at either end of the e......The necessary inertia compensation used in the force balance for the filament stretching rheometer is derived for an arbitrary frame of reference. This enables the force balance to be used to extract correctly the extensional viscosity from measurements of the tensile force at either end...

  4. Hybrid compensation arrangement in dispersed generation systems

    DEFF Research Database (Denmark)

    Chen, Zhe; Blaabjerg, Frede; Pedersen, John Kim

    2005-01-01

    This paper presents a hybrid compensation system consisting of an active filter and distributed passive filters. In the system, each individual passive filter is connected to a distortion source and designed to eliminate main harmonics and supply reactive power for the distortion source, while...... are performed for a power system including the dispersed generation units connected into the system through power electronic converters and diode rectifier loads, which produce the distorted waveforms. The simulation results have demonstrated that good compensation effects can be achieved by using the combined...

  5. Beam loading compensation in the NLCTA

    International Nuclear Information System (INIS)

    In the design of the Next Linear Collider (NLC), multi-bunch operation is employed to improve efficiency at the cost of substantial beam loading. The RF pulse that powers the accelerator structures will be shaped to compensate for the effect of the transient loading along the bunch train. This scheme has been implemented in the Next Linear Collider Test Accelerator (NLCTA), a facility built to test the key accelerator technology of the NLC. In this paper the authors describe the compensation method, the techniques used to measure the energy variation along the bunch train, and results from tests with NLC-like beam currents

  6. Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.

    Science.gov (United States)

    Gagnon, Jessica K; Law, Sean M; Brooks, Charles L

    2016-03-30

    Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an interconverting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs.

  7. 9 CFR 355.15 - Inedible material operating and storage rooms; outer premises, docks, driveways, etc.; fly...

    Science.gov (United States)

    2010-01-01

    ... storage rooms; outer premises, docks, driveways, etc.; fly-breeding material; nuisances. 355.15 Section....15 Inedible material operating and storage rooms; outer premises, docks, driveways, etc.; fly... any material in which flies may breed, or the maintenance of any nuisance on the premises shall not...

  8. Docking and 3-D QSAR studies on the binding of tetrahydropyrimid-2-one HIV-1 protease inhibitors

    Science.gov (United States)

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

    2013-06-01

    We present molecular docking and 3-D QSAR studies on a series of tetrahydropyrimid-2-one HIV-1 protease inhibitors whose binding affinities to the enzyme span nearly 6 orders of magnitude. The docking investigations have been carried out with Surflex (GEOM, GEOMX) and Glide (SP and XP) methodologies available through Tripos and Schrodinger suite of tools in the context of Sybyl-X and Maestro interfaces, respectively. The alignments for 3-D QSAR studies were obtained by using the automated Surflex-SIM methodology in Sybyl-X and the analyses were performed using the CoMFA and CoMSIA methods. Additionally, the top-ranked poses obtained from various docking protocols were also employed to generate CoMFA and CoMSIA models to evaluate the qualitative consistency of the docked models with experimental data. Our studies demonstrate that while there are a number of common features in the docked models obtained from Surflex-dock and Glide methodologies, the former sets of models are generally better correlated with deduced experimental binding modes based on the X-ray structures of known HIV-1 protease complexes with cyclic ureas. The urea moiety common to all the ligands are much more tightly aligned in Surflex docked structures than in the models obtained from Glide SP and XP dockings. The 3-D QSAR models are qualitatively and quantitatively similar to those previously reported, suggesting the utility of automatically generated alignments from Surflex-SIM methodology.

  9. Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.

    Science.gov (United States)

    Gagnon, Jessica K; Law, Sean M; Brooks, Charles L

    2016-03-30

    Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein flexibility. Proteins exist in an interconverting ensemble of conformational states, but effectively and efficiently searching the conformational space available to both the receptor and ligand remains a well-appreciated computational challenge. To this end, we have developed the Flexible CDOCKER method as an extension of the family of complete docking solutions available within CHARMM. This method integrates atomically detailed side chain flexibility with grid-based docking methods, maintaining efficiency while allowing the protein and ligand configurations to explore their conformational space simultaneously. This is in contrast to existing approaches that use induced-fit like sampling, such as Glide or Autodock, where the protein or the ligand space is sampled independently in an iterative fashion. Presented here are developments to the CHARMM docking methodology to incorporate receptor flexibility and improvements to the sampling protocol as demonstrated with re-docking trials on a subset of the CCDC/Astex set. These developments within CDOCKER achieve docking accuracy competitive with or exceeding the performance of other widely utilized docking programs. PMID:26691274

  10. Recessive mutations in DOCK6, encoding the guanidine nucleotide exchange factor DOCK6, lead to abnormal actin cytoskeleton organization and Adams-Oliver syndrome.

    Science.gov (United States)

    Shaheen, Ranad; Faqeih, Eissa; Sunker, Asma; Morsy, Heba; Al-Sheddi, Tarfa; Shamseldin, Hanan E; Adly, Nouran; Hashem, Mais; Alkuraya, Fowzan S

    2011-08-12

    Adams-Oliver syndrome (AOS) is defined by the combination of aplasia cutis congenita (ACC) and terminal transverse limb defects (TTLD). It is usually inherited as an autosomal-dominant trait, but autosomal-recessive inheritance has also been documented. In an individual with autosomal-recessive AOS, we combined autozygome analysis with exome sequencing to identify a homozygous truncating mutation in dedicator of cytokinesis 6 gene (DOCK6) which encodes an atypical guanidine exchange factor (GEF) known to activate two members of the Rho GTPase family: Cdc42 and Rac1. Another homozygous truncating mutation was identified upon targeted sequencing of DOCK6 in an unrelated individual with AOS. Consistent with the established role of Cdc42 and Rac1 in the organization of the actin cytoskeleton, we demonstrate a cellular phenotype typical of a defective actin cytoskeleton in patient cells. These findings, combined with a Dock6 expression profile that is consistent with an AOS phenotype as well as the very recent demonstration of dominant mutations of ARHGAP31 in AOS, establish Cdc42 and Rac1 as key molecules in the pathogenesis of AOS and suggest that other regulators of these Rho GTPase proteins might be good candidates in the quest to define the genetic spectrum of this genetically heterogeneous condition.

  11. Application of fuzzy logic-neural network based reinforcement learning to proximity and docking operations: Special approach/docking testcase results

    Science.gov (United States)

    Jani, Yashvant

    1993-01-01

    As part of the RICIS project, the reinforcement learning techniques developed at Ames Research Center are being applied to proximity and docking operations using the Shuttle and Solar Maximum Mission (SMM) satellite simulation. In utilizing these fuzzy learning techniques, we use the Approximate Reasoning based Intelligent Control (ARIC) architecture, and so we use these two terms interchangeably to imply the same. This activity is carried out in the Software Technology Laboratory utilizing the Orbital Operations Simulator (OOS) and programming/testing support from other contractor personnel. This report is the final deliverable D4 in our milestones and project activity. It provides the test results for the special testcase of approach/docking scenario for the shuttle and SMM satellite. Based on our experience and analysis with the attitude and translational controllers, we have modified the basic configuration of the reinforcement learning algorithm in ARIC. The shuttle translational controller and its implementation in ARIC is described in our deliverable D3. In order to simulate the final approach and docking operations, we have set-up this special testcase as described in section 2. The ARIC performance results for these operations are discussed in section 3 and conclusions are provided in section 4 along with the summary for the project.

  12. Assessing molecular docking tools for relative biological activity prediction: a case study of triazole HIV-1 NNRTIs.

    Science.gov (United States)

    Frączek, Tomasz; Siwek, Agata; Paneth, Piotr

    2013-12-23

    Molecular docking is a technique widely used in drug design. Many studies exist regarding the general accuracy of various docking programs, but case studies for a given group of related compounds are rare. In order to facilitate identification of novel triazole HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), several docking and scoring programs were evaluated for their ability to predict relative biological activity of 111 known 1,2,4-triazole and 76 other azole type NNRTIs. Glide, FlexX, Molegro Virtual Docker, AutoDock Vina, and Hyde were used. Different protocols, settings, scoring functions, and interaction terms were analyzed. We have found that the programs performance was dependent on the data set, indicating the importance of choosing good quality target data for any comparative study. The results suggest that after optimization and proper validation, some of the molecular docking programs can help in predicting relative biological activity of azole NNRTIs. PMID:24266618

  13. Compensations in the Shapley value and the compensation solutions for graph games

    OpenAIRE

    Béal, Sylvain; Rémila, Eric; Solal, Philippe

    2010-01-01

    We consider an alternative expression of the Shapley value that reveals a system of compensations: each player receives an equal share of the worth of each coalition he belongs to, and has to compensate an equal share of the worth of any coalition he does not belong to. We give an interpretation in terms of formation of the grand coalition according to an ordering of the players and define the corresponding compensation vector. Then, we generalize this idea to cooperative games with a communi...

  14. Large PMD Compensated by Four Free Degrees in OTDM System

    Institute of Scientific and Technical Information of China (English)

    LUO Rui; LI Tang-jun; WANG Mu-guang; JIAN Shui-sheng; XU Jing-jing

    2004-01-01

    By introducing a two-stage polarization mode dispersion (PMD) compensator after a optical fiber link with a large PMD,over 270 ps first-order and 2 000 ps2 high-order PMD was compensated. The results show that the two-stage compensator can be used to PMD compensation in the 20 Gb/s optical time division multiplexing system with 60 km high PMD fiber. After compensating,the 270 ps DGD is changed into max. 7 ps. Moreover,the tunable FBG has a function of dispersion compensation.

  15. T1 VSAT Fade Compensation Statistical Results

    Science.gov (United States)

    Johnson, Sandra K.; Acosta, Roberto; Ugweje, Oke

    2000-01-01

    New satellite communication systems are steadily seeking to use higher frequency bands to accommodate the requirements for additional capacity. At these higher frequencies, propagation impairments that did not significantly affect the signal at lower frequencies begin to have considerable impact. In Ka-band. the next logical commercial frequency band to be used for satellite communication, attenuation of the signal due to rain is a primary concern. An experimental satellite built by NASA, the Advanced Communication Technology Satellite (ACTS). launched in September 1993, is the first U.S. communication satellite operating in the Ka-band. In addition to higher carrier frequencies, a number of other new technologies, including on-board baseband processing. multiple beam antennas, and rain fade detection and compensation techniques, were designed into the ACTS. Verification experiments have been conducted since the launch to characterize the new technologies. The focus of this paper is to characterize the method used by the ACTS TI Very Small Aperture Terminal (TI VSAT) ground stations in detecting the presence of fade in the communication signal and to adaptively compensate for it by the addition of burst rate reduction and forward error correction. Measured data obtained from the ACTS program was used to validate the compensation technique. A software process was developed and demonstrated to statistically characterize the increased availability achieved by the compensation techniques in terms of the bit error rate time enhancement factor. Several improvements to the ACTS technique are discussed and possible implementations for future Ka band system are offered.

  16. The cost and compensability of trauma patients.

    Science.gov (United States)

    Curtis, Kate; Dickson, Cara; Black, Deborah; Nau, Thomas

    2009-02-01

    Injury in Australia was responsible for 400 000 hospitalisations in 2002. This study aimed to examine the direct costs of trauma patients in a Level 1 trauma centre and determine the compensability of those patients. Data on all admitted patients (206) filling trauma criteria were collected prospectively over a 3-month period (November 2006 to January 2007). A 10-question survey was completed on each patient to record mechanism of injury, third party private health insurance or workers compensation, and direct costs were also obtained. 30% of trauma admissions had an injury severity score (ISS)> 15 (n = 62; median ISS =9; range, 1-56). Median length of stay was 3 days (range, 1-126). Almost half (47%) of the patients were involved in road trauma, and 29% in falls. More than half (53.4%) were eligible for compensation (21.8% of patients had full hospital health insurance cover, 21.4% third party insurance and 9.2% workers compensation). The mechanism of injury with the highest median cost per patient was assault, followed by pedal cyclists, pedestrians then motor vehicle collisions. PMID:19203337

  17. Externalities and Compensation : Primeval Games and Solutions

    NARCIS (Netherlands)

    Ju, Y.; Borm, P.E.M.

    2005-01-01

    The classical literature (Pigou (1920), Coase (1960), Arrow (1970)) and the relatively recent studies (cf.Varian (1994)) associate the externality problem with efficiency.This paper focuses explicitly on the compensation problem in the context of externalities.To capture the features of inter-indivi

  18. Compensation for forest ecological services in China

    Institute of Scientific and Technical Information of China (English)

    Liu Can; Wang Sen; Zhang Wei; Liang Dan

    2007-01-01

    The paper discusses methods to compensate for the costs incurred in the supply of forest ecological services (FES), i.e.government dominated and market-based instruments as well as progress made so far in China. Factors which constrain the supply of these services and potential policy improvements are presented.

  19. 12 CFR 2.5 - Bank compensation.

    Science.gov (United States)

    2010-01-01

    ... the bank's loan customers. (b) Income derived from credit life insurance sales to loan customers may... seq., or to a trust for the benefit of all shareholders, provided that the bank receives reasonable... 12 Banks and Banking 1 2010-01-01 2010-01-01 false Bank compensation. 2.5 Section 2.5 Banks...

  20. PRECISELY COMPENSATED EFFICIENT COMPONENT MODE SYNTHESIS METHOD

    Institute of Scientific and Technical Information of China (English)

    Zhu Yutian; Ichiro Hagiwara

    2004-01-01

    Based on the improved mode superposition method proposed by Z.D.Ma and I.Hagiwara, a precisely compensated efficient mode synthesis method is developed.The calculation procedure is discussed in detail and the truncation error is also analyzed.By comparison, it is shown that this method has a higher accuracy and a less calculation time than the general used ones.

  1. 76 FR 27959 - Investment Adviser Performance Compensation

    Science.gov (United States)

    2011-05-13

    ... for Advisers to Venture Capital Funds, Private Fund Advisers With Less Than $150 Million in Assets... compensation to the adviser based on a share of capital gains on, or capital appreciation of, the funds of a... or Fund Under Management is Averaged, Investment Advisers Act Release No. 347 (Nov. 10, 1972) [37...

  2. Executive Compensation and the Cost of Debt

    NARCIS (Netherlands)

    Kabir, Rezaul; Li, Hao; Veld-Merkoulova, Yulia V.

    2010-01-01

    We examine how executive compensation affects the cost of debt financing. Analyzing CEO pay data from the UK, we find that debt-like and equity-like pay components have opposite effects on the cost of debt. An increase in defined benefit pensions is associated with lower bond yield spread, while an

  3. Digital compensation of nonlinear distortion in loudspeakers

    NARCIS (Netherlands)

    Vries, de Ruurd; Berkhoff, Arthur P.; Slump, Cornelis H.; Herrmann, Otto E.

    1993-01-01

    Loudspeakers produce nonlinear distortion. The authors present a method to compensate for this distortion in real time by nonlinear digital signal processing implemented on a digital signal processor (i.e., the TMS320C30 DSP). Based on the literature, an electrical equivalent circuit of an electrody

  4. Large Capacity SMES for Voltage Dip Compensation

    Science.gov (United States)

    Iwatani, Yu; Saito, Fusao; Ito, Toshinobu; Shimada, Mamoru; Ishida, Satoshi; Shimanuki, Yoshio

    Voltage dips of power grids due to thunderbolts, snow damage, and so on, cause serious damage to production lines of precision instruments, for example, semiconductors. In recent years, in order to solve this problem, uninterruptible power supply systems (UPS) are used. UPS, however, has small capacity, so a great number of UPS are needed in large factories. Therefore, we have manufactured the superconducting magnetic energy storage (SMES) system for voltage dip compensation able to protect loads with large capacity collectively. SMES has advantages such as space conservation, long lifetime and others. In field tests, cooperating with CHUBU Electric Power Co., Inc. we proved that SMES is valuable for compensating voltage dips. Since 2007, 10MVA SMES improved from field test machines has been running in a domestic liquid crystal display plant, and in 2008, it protected plant loads from a number of voltage dips. In this paper, we report the action principle and components of the improved SMES for voltage dip compensation, and examples of waveforms when 10MVA SMES compensated voltage dips.

  5. On compensation in multidimensional response modeling

    NARCIS (Netherlands)

    Linden, van der W.J.

    2012-01-01

    The issue of compensation in multidimensional response modeling is addressed. We show that multidimensional response models are compensatory in their ability parameters if and only if they are monotone. In addition, a minimal set of assumptions is presented under which the MLEs of the ability parame

  6. On the compensation effect in heterogeneous catalysis

    DEFF Research Database (Denmark)

    Pedersen, Thomas Bligaard; Honkala, Johanna Karoliina; Logadottir, Ashildur;

    2003-01-01

    For a class of heterogeneously catalyzed reactions, we explain the compensation effect in terms of a switching of kinetic regimes leading to a concomitant change in the apparent activation energy and in the prefactor for the overall rate of the reaction. We first use the ammonia synthesis to illu...

  7. Fish-mediated trait compensation in zooplankton

    DEFF Research Database (Denmark)

    Hylander, Samuel; Souza, M.S.; Balseiro, E.;

    2012-01-01

    pigmentation and antioxidant enzymes are flexible UVR defence systems, which can be induced when needed. Zooplankton may employ antioxidant defences when pigmentation is reduced to counteract predation risk and thereby rapidly respond to detrimental effects of UVR exposure, that is, they can compensate one...

  8. Disclosed Values of Option-Based Compensation

    DEFF Research Database (Denmark)

    Bechmann, Ken L.; Hjortshøj, Toke Lilhauge

    New accounting standards require firms to expense the costs of option-based compensation (OBC), but the associated valuations offer many challenges for firms. Earlier research has documented that firms in the U.S. generally underreport the values of OBC by manipulating the inputs used for valuation...

  9. Fuel viscosity/density compensation device

    Energy Technology Data Exchange (ETDEWEB)

    Bostwick, N.W.

    1989-12-26

    This patent describes a fuel viscosity compensating device for providing an output which may be used to regulate the output of a fuel pump based on the viscosity of the fuel. It comprises: a housing including walls defining a pressure chamber and a fuel inlet; a piston; a piston spring; a pressure regulator; conduit means; swirl means; and fuel control means.

  10. Granulate of stainless steel as compensator material

    NARCIS (Netherlands)

    J.P.C. van Santvoort (J. P C)

    1995-01-01

    textabstractCompensators produced with computer controlled milling devices usually consist of a styrofoam mould, filled with an appropriate material. We investigated granulate of stainless steel as filling material. This cheap, easy to use, clean and re-usable material can be obtained with an averag

  11. Molecular docking of bacosides with tryptophan hydroxylase: a model to understand the bacosides mechanism.

    Science.gov (United States)

    Rajathei, David Mary; Preethi, Jayakumar; Singh, Hemant K; Rajan, Koilmani Emmanuvel

    2014-08-01

    Tryptophan hydroxylase (TPH) catalyses l-tryptophan into 5-hydroxy-l-tryptophan, which is the first and rate-limiting step of serotonin (5-HT) biosynthesis. Earlier, we found that TPH2 up-regulated in the hippocampus of postnatal rats after the oral treatment of Bacopa monniera leaf extract containing the active compound bacosides. However, the knowledge about the interactions between bacosides with TPH is limited. In this study, we take advantage of in silico approach to understand the interaction of bacoside-TPH complex using three different docking algorithms such as HexDock, PatchDock and AutoDock. All these three algorithms showed that bacoside A and A3 well fit into the cavity consists of active sites. Further, our analysis revealed that major active compounds bacoside A3 and A interact with different residues of TPH through hydrogen bond. Interestingly, Tyr235, Thr265 and Glu317 are the key residues among them, but none of them are either at tryptophan or BH4 binding region. However, its note worthy to mention that Tyr 235 is a catalytic sensitive residue, Thr265 is present in the flexible loop region and Glu317 is known to interacts with Fe. Interactions with these residues may critically regulate TPH function and thus serotonin synthesis. Our study suggested that the interaction of bacosides (A3/A) with TPH might up-regulate its activity to elevate the biosynthesis of 5-HT, thereby enhances learning and memory formation.

  12. Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

    Directory of Open Access Journals (Sweden)

    Esquivel-Rodríguez Juan

    2012-03-01

    Full Text Available Abstract Background Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights. Methods We generated a series of predicted models (decoys of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys. Results and conclusion We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å as fpair and propose to use it for evaluation of the accuracy of multiple protein docking.

  13. A robot to detect and control broad-leaved dock (Rumex obtusifolius L.) in grassland

    NARCIS (Netherlands)

    Evert, van F.K.; Samsom, J.; Polder, G.; Vijn, M.P.; Dooren, van H.J.C.; Lamaker, E.J.J.; Heijden, van der G.W.A.M.; Kempenaar, C.; Zalm, van der A.J.A.; Lotz, L.A.P.

    2011-01-01

    Broad-leaved dock is a common and troublesome grassland weed with a wide geographic distribution. In conventional farming the weed is normally controlled by using a selective herbicide, but in organic farming manual removal is the best option to control this weed. The objective of our work was to de

  14. The binding of cytochrome c to neuroglobin: A docking and surface plasmon resonance study

    DEFF Research Database (Denmark)

    Bønding, Signe Helbo; Henty, K.; Dingley, A.J.;

    2008-01-01

    It has recently been proposed that the role of neuroglobin in the protection of neurons from ischaemia induced cell death requires the formation of a transient complex with cytochrome c. No such complex has yet been isolated. Here, we present the results of soft docking calculations, which indica...

  15. Molecular Docking of Enzyme Inhibitors: A Computational Tool for Structure-Based Drug Design

    Science.gov (United States)

    Rudnitskaya, Aleksandra; Torok, Bela; Torok, Marianna

    2010-01-01

    Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise…

  16. Virtual Screening and Docking Studies of Synthesized Chalcones: Potent Anti-Malarial Drug

    Directory of Open Access Journals (Sweden)

    Prashant Singh

    2016-03-01

    Full Text Available A novel series of Chalcones were synthesized targets asexual blood stages of Plasmodium falciparum has been analyzed by utilizing a combination of molecular modeling techniques. Statistically significant structure-based quantitative structure activity relationships models were generated and validated through acceptable predictive ability to support internal and external set of compounds. Screening of most valuable drug among of pre-synthesized drug on the basis of binding efficiency to target receptor was carried out by docking view. Prior this pre-computed Mean IC50 and MIC value were also taken in consideration. The most effective compound on the basis all consideration was found. Previous studies have suggested that Ca2+-ATPase (PfATP6 of P. falciparum is the target of many anti-malarial drugs. However, the mechanism of inhibition of Ca2+- ATPase (PfATP6 is not known. Here we address this issue using bioinformatics tools. We generated a molecular model of Ca2+-ATPase (PfATP6 of P. falciparum and performed molecular docking of all chalcones. Molecular docking programme Glide iGEMDock was used to determine binding feasibility of 52 analogues of chalcones. The comparison of docking parameters showed, more than 5 analogues are better ligands of PfATP6. The binding of chalocones to PFATP6 is mediated by both hydrogen bonding, hydrophobic and polar interactions. Our results suggest that chalcones analogues are promising lead compounds for the development of anti-malarial drugs

  17. 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.

  18. Implementation of Statistical Process Control: Evaluating the Mechanical Performance of a Candidate Silicone Elastomer Docking Seal

    Science.gov (United States)

    Oravec, Heather Ann; Daniels, Christopher C.

    2014-01-01

    The National Aeronautics and Space Administration has been developing a novel docking system to meet the requirements of future exploration missions to low-Earth orbit and beyond. A dynamic gas pressure seal is located at the main interface between the active and passive mating components of the new docking system. This seal is designed to operate in the harsh space environment, but is also to perform within strict loading requirements while maintaining an acceptable level of leak rate. In this study, a candidate silicone elastomer seal was designed, and multiple subscale test articles were manufactured for evaluation purposes. The force required to fully compress each test article at room temperature was quantified and found to be below the maximum allowable load for the docking system. However, a significant amount of scatter was observed in the test results. Due to the stochastic nature of the mechanical performance of this candidate docking seal, a statistical process control technique was implemented to isolate unusual compression behavior from typical mechanical performance. The results of this statistical analysis indicated a lack of process control, suggesting a variation in the manufacturing phase of the process. Further investigation revealed that changes in the manufacturing molding process had occurred which may have influenced the mechanical performance of the seal. This knowledge improves the chance of this and future space seals to satisfy or exceed design specifications.

  19. Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.

    Science.gov (United States)

    Iakovou, Georgios; Hayward, Steven; Laycock, Stephen D

    2015-09-01

    Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates.

  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. Identification of Novel Aldose Reductase Inhibitors from Spices: A Molecular Docking and Simulation Study.

    Science.gov (United States)

    Antony, Priya; Vijayan, Ranjit

    2015-01-01

    Hyperglycemia in diabetic patients results in a diverse range of complications such as diabetic retinopathy, neuropathy, nephropathy and cardiovascular diseases. The role of aldose reductase (AR), the key enzyme in the polyol pathway, in these complications is well established. Due to notable side-effects of several drugs, phytochemicals as an alternative has gained considerable importance for the treatment of several ailments. In order to evaluate the inhibitory effects of dietary spices on AR, a collection of phytochemicals were identified from Zingiber officinale (ginger), Curcuma longa (turmeric) Allium sativum (garlic) and Trigonella foenum graecum (fenugreek). Molecular docking was performed for lead identification and molecular dynamics simulations were performed to study the dynamic behaviour of these protein-ligand interactions. Gingerenones A, B and C, lariciresinol, quercetin and calebin A from these spices exhibited high docking score, binding affinity and sustained protein-ligand interactions. Rescoring of protein ligand interactions at the end of MD simulations produced binding scores that were better than the initially docked conformations. Docking results, ligand interactions and ADMET properties of these molecules were significantly better than commercially available AR inhibitors like epalrestat, sorbinil and ranirestat. Thus, these natural molecules could be potent AR inhibitors.

  2. Study on dock nuclear emergency decision-making model based on theory of bayes risk decision

    International Nuclear Information System (INIS)

    Considering the characteristics of nuclear power ship dock and in order to reduce the effect brought about by the uncertainty of wind field, optimization model has been established based on Bayes risk decision theory. The model compartmentalizes a whole area into several subfields and further takes into account the restriction of public acceptability and international intervention principle. An example analysis is also provided. (authors)

  3. Identification of Novel Aldose Reductase Inhibitors from Spices: A Molecular Docking and Simulation Study.

    Science.gov (United States)

    Antony, Priya; Vijayan, Ranjit

    2015-01-01

    Hyperglycemia in diabetic patients results in a diverse range of complications such as diabetic retinopathy, neuropathy, nephropathy and cardiovascular diseases. The role of aldose reductase (AR), the key enzyme in the polyol pathway, in these complications is well established. Due to notable side-effects of several drugs, phytochemicals as an alternative has gained considerable importance for the treatment of several ailments. In order to evaluate the inhibitory effects of dietary spices on AR, a collection of phytochemicals were identified from Zingiber officinale (ginger), Curcuma longa (turmeric) Allium sativum (garlic) and Trigonella foenum graecum (fenugreek). Molecular docking was performed for lead identification and molecular dynamics simulations were performed to study the dynamic behaviour of these protein-ligand interactions. Gingerenones A, B and C, lariciresinol, quercetin and calebin A from these spices exhibited high docking score, binding affinity and sustained protein-ligand interactions. Rescoring of protein ligand interactions at the end of MD simulations produced binding scores that were better than the initially docked conformations. Docking results, ligand interactions and ADMET properties of these molecules were significantly better than commercially available AR inhibitors like epalrestat, sorbinil and ranirestat. Thus, these natural molecules could be potent AR inhibitors. PMID:26384019

  4. Identification of Novel Aldose Reductase Inhibitors from Spices: A Molecular Docking and Simulation Study.

    Directory of Open Access Journals (Sweden)

    Priya Antony

    Full Text Available Hyperglycemia in diabetic patients results in a diverse range of complications such as diabetic retinopathy, neuropathy, nephropathy and cardiovascular diseases. The role of aldose reductase (AR, the key enzyme in the polyol pathway, in these complications is well established. Due to notable side-effects of several drugs, phytochemicals as an alternative has gained considerable importance for the treatment of several ailments. In order to evaluate the inhibitory effects of dietary spices on AR, a collection of phytochemicals were identified from Zingiber officinale (ginger, Curcuma longa (turmeric Allium sativum (garlic and Trigonella foenum graecum (fenugreek. Molecular docking was performed for lead identification and molecular dynamics simulations were performed to study the dynamic behaviour of these protein-ligand interactions. Gingerenones A, B and C, lariciresinol, quercetin and calebin A from these spices exhibited high docking score, binding affinity and sustained protein-ligand interactions. Rescoring of protein ligand interactions at the end of MD simulations produced binding scores that were better than the initially docked conformations. Docking results, ligand interactions and ADMET properties of these molecules were significantly better than commercially available AR inhibitors like epalrestat, sorbinil and ranirestat. Thus, these natural molecules could be potent AR inhibitors.

  5. A Memetic Algorithm for the Vehicle Routing Problem with Cross Docking

    Directory of Open Access Journals (Sweden)

    Sanae Larioui

    2015-11-01

    Full Text Available In this paper we address the VRPCD, in which a set of homogeneous vehicles are used to transport products from the suppliers to customers via a cross-dock. The products can be consolidated at the cross-dock but cannot be stored for very long as the cross-dock does not have long-term inventory-holding capabilities. The objective of the VRPCD is to minimize the total traveled distance while respecting time window constraints of suppliers and customers and a time horizon for the whole transportation operation. Rummaging through all the work of literature on vehicle routing problems with cross-docking, there is no work that considers that customer will receive its requests from several suppliers; this will be the point of innovation of this work. A heuristic and a memetic algorithm are used to solve the problem. The proposed algorithms are implemented and tested on data sets involving up to 200 nodes (customers and suppliers. The first results show that the memetic algorithm can produce high quality solutions.

  6. Drug targets for cell cycle dysregulators in leukemogenesis: in silico docking studies.

    Directory of Open Access Journals (Sweden)

    Archana Jayaraman

    Full Text Available Alterations in cell cycle regulating proteins are a key characteristic in neoplastic proliferation of lymphoblast cells in patients with Acute Lymphoblastic Leukemia (ALL. The aim of our study was to investigate whether the routinely administered ALL chemotherapeutic agents would be able to bind and inhibit the key deregulated cell cycle proteins such as--Cyclins E1, D1, D3, A1 and Cyclin Dependent Kinases (CDK 2 and 6. We used Schrödinger Glide docking protocol to dock the chemotherapeutic drugs such as Doxorubicin and Daunorubicin and others which are not very common including Clofarabine, Nelarabine and Flavopiridol, to the crystal structures of these proteins. We observed that the drugs were able to bind and interact with cyclins E1 and A1 and CDKs 2 and 6 while their docking to cyclins D1 and D3 were not successful. This binding proved favorable to interact with the G1/S cell cycle phase proteins that were examined in this study and may lead to the interruption of the growth of leukemic cells. Our observations therefore suggest that these drugs could be explored for use as inhibitors for these cell cycle proteins. Further, we have also highlighted residues which could be important in the designing of pharmacophores against these cell cycle proteins. This is the first report in understanding the mechanism of action of the drugs targeting these cell cycle proteins in leukemia through the visualization of drug-target binding and molecular docking using computational methods.

  7. 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

  8. Just-in-Time Retail Distribution : A Systems Perspective on Cross-Docking

    NARCIS (Netherlands)

    Buijs, Paul; Danhof, Hans W.; Wortmann, J.(Hans) C.

    2016-01-01

    Cross-docking is a just-in-time strategy for distribution logistics. It is aimed at reducing inventory levels and distribution lead times by creating a seamless flow of products from suppliers to customers. Prior supply chain literature has argued that creating such a seamless product flows requires

  9. Molecular docking of bacosides with tryptophan hydroxylase: a model to understand the bacosides mechanism.

    Science.gov (United States)

    Rajathei, David Mary; Preethi, Jayakumar; Singh, Hemant K; Rajan, Koilmani Emmanuvel

    2014-08-01

    Tryptophan hydroxylase (TPH) catalyses l-tryptophan into 5-hydroxy-l-tryptophan, which is the first and rate-limiting step of serotonin (5-HT) biosynthesis. Earlier, we found that TPH2 up-regulated in the hippocampus of postnatal rats after the oral treatment of Bacopa monniera leaf extract containing the active compound bacosides. However, the knowledge about the interactions between bacosides with TPH is limited. In this study, we take advantage of in silico approach to understand the interaction of bacoside-TPH complex using three different docking algorithms such as HexDock, PatchDock and AutoDock. All these three algorithms showed that bacoside A and A3 well fit into the cavity consists of active sites. Further, our analysis revealed that major active compounds bacoside A3 and A interact with different residues of TPH through hydrogen bond. Interestingly, Tyr235, Thr265 and Glu317 are the key residues among them, but none of them are either at tryptophan or BH4 binding region. However, its note worthy to mention that Tyr 235 is a catalytic sensitive residue, Thr265 is present in the flexible loop region and Glu317 is known to interacts with Fe. Interactions with these residues may critically regulate TPH function and thus serotonin synthesis. Our study suggested that the interaction of bacosides (A3/A) with TPH might up-regulate its activity to elevate the biosynthesis of 5-HT, thereby enhances learning and memory formation. PMID:25089244

  10. 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.

  11. Insights into the structural and functional aspects of rela by molecular modeling and docking calculations.

    Digital Repository Service at National Institute of Oceanography (India)

    Nath I.V.A.; LokaBharathi, P.A.; Deobagkar, D.D.

    published in the second case. These models were subjected to docking calculations using ppGpp synthetic analogues.The binding pocket characteristics in RelA are prone to fluctuations due to changes in some crucial interacting residues and this can have a...

  12. 48 CFR 47.303-12 - Ex dock, pier, or warehouse, port of importation.

    Science.gov (United States)

    2010-10-01

    ... warehouse, port of importation. 47.303-12 Section 47.303-12 Federal Acquisition Regulations System FEDERAL..., pier, or warehouse, port of importation. (a) Explanation of delivery term. Ex dock, pier, or warehouse... in the warehouse at the specified port of importation. (b) Contractor responsibilities....

  13. PRESSURE COMPENSATION METHOD OF UNDERWATER HYDRAULIC SYSTEM WITH HYDRAULIC POWER UNIT BEING UNDER ATMOSPHERIC CIRCUMSTANCE AND PRESSURE COMPENSATED VALVE

    Institute of Scientific and Technical Information of China (English)

    Wang Qingfeng; Li Yanmin; Zhong Tianyu; Xu Guohua

    2005-01-01

    Based on the analysis of the-state-of-the-art of pressure compensation of underwater hydraulic systems (UHSs), a new method of pressure compensation of UHSs, whose hydraulic power unit is in the atmospheric circumstance, is proposed. And a pilot-operated relief valve with pressure compensation is realized. The pressure compensation precision is guaranteed by direct detection. Its dynamic performance and stability are improved by a dynamic feedback. Theoretical study, simulation and experiment show that the pilot-operated relief valve with pressure compensation has a fine property of tracking underwater ambient pressure and meet the requirement of underwater ambient pressure compensation.

  14. Compensation of errors in robot machining with a parallel 3D-piezo compensation mechanism

    OpenAIRE

    Schneider, Ulrich; Drust, Manuel; Puzik, Arnold; Verl, Alexander

    2013-01-01

    This paper proposes an approach for a 3D-Piezo Compensation Mechanism unit that is capable of fast and accurate adaption of the spindle position to enhance machining by robots. The mechanical design is explained which focuses on low mass, good stiffness and high bandwidth in order to allow compensating for errors beyond the bandwidth of the robot. In addition to previous works [7] and [9], an advanced actuation design is presented enabling movements in three translational axes allowing a work...

  15. Re-planning for compensator-based IMRT with original compensators.

    Science.gov (United States)

    Zhang, Geoffrey; Feygelman, Vladimir; Stevens, Craig; Li, Weiqi; Leuthold, Susan; Springett, Gregory; Hoffe, Sarah

    2011-01-01

    Compared with multileaf collimator (MLC)-based intensity-modulated radiotherapy (IMRT) for moving targets, compensator-based IMRT has advantages such as shorter beam-on time, fewer monitor units with potentially decreased secondary carcinogenesis risk, better optimization-to-deliverable dose conversion, and often better dose conformity. Some of the disadvantages include additional time for the compensators to be built and delivered, as well as extra cost. Patients undergoing treatment of abdominal cancers often experience weight loss. It would be necessary to account for this change in weight with a new plan and a second set of compensators. However, this would result in treatment delays and added costs. We have developed a method to re-plan the patient using the same set of compensators. Because the weight changes seen with the treatment of abdominal cancers are usually relatively small, a new 4D computed tomography (CT) acquired in the treatment position with markers on the original isocenter tattoos can be registered to the original planning scan. The contours of target volumes from the original scans are copied to the new scan after fusion. The original compensator set can be used together with a few field-in-field (FiF) beams defined by the MLC (or beams with cerrobend blocks for accelerators not equipped with a MLC). The weights of the beams with compensators are reduced so that the FiF or blocked beams can be optimized to mirror the original plan and dose distribution. Seven abdominal cancer cases are presented using this technique. The new plan on the new planning CT images usually has the same dosimetric quality as the original. The target coverage and dose uniformity are improved compared with the plan without FiF/block modification. Techniques combining additional FiF or blocked beams with the original compensators optimize the treatment plans when patients lose weight and save time and cost compared with generating plans with a new set of compensators.

  16. Deformation compensation in dynamic tomography; Compensation de deformations en tomographie dynamique

    Energy Technology Data Exchange (ETDEWEB)

    Desbat, L. [Universite Joseph Fourier, UMR CNRS 5525, 38 - Grenoble (France); Roux, S. [Universite Joseph Fourier, TIMC-IMAG, In3S, Faculte de Medecine, 38 - Grenoble (France)]|[CEA Grenoble, Lab. d' Electronique et de Technologie de l' Informatique (LETI), 38 (France); Grangeat, P. [CEA Grenoble, Lab. d' Electronique et de Technologie de l' Informatique (LETI), 38 (France)

    2005-07-01

    This work is a contribution to the compensation of motion in tomography. New classes of deformation are proposed, that compensates analytically by an algorithm of a F.B.P. type reconstruction. This work makes a generalisation of the known results for affine deformations, in parallel geometry and fan-beam, to deformation classes of infinite dimension able to include strong non linearities. (N.C.)

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

    Directory of Open Access Journals (Sweden)

    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.

  18. [Study on anti-hyperlipidemia mechanism of high frequency herb pairs by molecular docking method].

    Science.gov (United States)

    Jiang, Lu-di; He, Yu-su; Chen, Xi; Tao, Ou; Li, Gong-Yu; Zhang, Yan-ling

    2015-06-01

    Traditional Chinese medicine (TCM) has definitely clinical effect in treating hyperlipidemia, but the action mechanism still need to be explored. Based on consulting Chinese Pharmacopoeia (2010), all the lipid-lowering Chinese patent medicines were analyzed by associated rules data mining method to explore high frequency herb pairs. The top three couplet medicines with high support degree were Puerariae Lobatae Radix-Crataegi Fructus, Salviae Miltiorrhizae Radix et Rhizoma-Crataegi Fructus, and Polygoni Multiflori Radix-Crataegi Fructus. The 20 main ingredients were selected from the herb pairs and docked with 3 key hyperlipidemia targets, namely 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase), peroxisome proliferator activated receptor-α (PPAR-α ) and niemann-pick C1 like 1 (NPC1L1) to further discuss the molecular mechanism of the high frequency herb pairs, by using the docking program, LibDock. To construct evaluation rules for the ingredients of herb pairs, the root-mean-square deviation (RMSD) value between computed and initial complexes was first calculated to validate the fitness of LibDock models. Then, the key residues were also confirmed by analyzing the interactions of those 3 proteins and corresponding marketed drugs. The docking results showed that hyperin, puerarin, salvianolic acid A and polydatin can interact with two targets, and the other five compounds may be potent for at least one of the three targets. In this study, the multi-target effect of high frequency herb pairs for lipid-lowering was discussed on the molecular level, which can help further researching new multi-target anti-hyperlipidemia drug.

  19. MTB-USDH Compensation Tracking System (MTB-CTS)

    Data.gov (United States)

    US Agency for International Development — MTB-USDH Compensation Tracking System: is the USDH Compensation Tracking System (MTB-CTS) to assist managers in monitoring their payroll costs for U.S. direct...

  20. The risks and rewards of setting physician compensation internally.

    Science.gov (United States)

    Johnson, Jen

    2013-01-01

    To establish physician compensation internally, finance leaders should: Educate decision makers on basic regulatory guidance and valuation theory. Determine fair market value. Consider using a compensation calculator. PMID:23360054