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Sample records for homology modeling server

  1. A Capacity Supply Model for Virtualized Servers

    Directory of Open Access Journals (Sweden)

    Alexander PINNOW

    2009-01-01

    Full Text Available This paper deals with determining the capacity supply for virtualized servers. First, a server is modeled as a queue based on a Markov chain. Then, the effect of server virtualization on the capacity supply will be analyzed with the distribution function of the server load.

  2. PRIMO: An Interactive Homology Modeling Pipeline

    Science.gov (United States)

    Glenister, Michael

    2016-01-01

    The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/. PMID:27855192

  3. PRIMO: An Interactive Homology Modeling Pipeline.

    Science.gov (United States)

    Hatherley, Rowan; Brown, David K; Glenister, Michael; Tastan Bishop, Özlem

    2016-01-01

    The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO's automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.

  4. A polling model with an autonomous server

    NARCIS (Netherlands)

    Haan, de Roland; Boucherie, Richard J.; Ommeren, van Jan-Kees C.W.

    2007-01-01

    Polling models are used as an analytical performance tool in several application areas. In these models, the focus often is on controlling the operation of the server as to optimize some performance measure. For several applications, controlling the server is not an issue as the server moves indepen

  5. A polling model with an autonomous server

    OpenAIRE

    2007-01-01

    Polling models are used as an analytical performance tool in several application areas. In these models, the focus often is on controlling the operation of the server as to optimize some performance measure. For several applications, controlling the server is not an issue as the server moves independently in the system. We present the analysis for such a polling model with a so-called autonomous server. In this model, the server remains for an exogenous random time at a queue, which also impl...

  6. RCD+: Fast loop modeling server.

    Science.gov (United States)

    López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

    2016-07-08

    Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Cluster based on sequence comparison of homologous proteins of 95 organism species - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Gclust Server Cluster based on sequence comparison of homologous proteins of 95 organism species Data detail... Data name Cluster based on sequence comparison of homologous proteins of 95 organism species Description of...e History of This Database Site Policy | Contact Us Cluster based on sequence comparison of homologous proteins of 95 organism species - Gclust Server | LSDB Archive ...

  8. BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.

    Science.gov (United States)

    Paz, Inbal; Kligun, Efrat; Bengad, Barak; Mandel-Gutfreund, Yael

    2016-07-08

    Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with yet another known function, are awaiting to be discovered. Here we present a new web server, BindUP, freely accessible through the website http://bindup.technion.ac.il/, for predicting DNA and RNA binding proteins using a non-homology-based approach. Our method is based on the electrostatic features of the protein surface and other general properties of the protein. BindUP predicts nucleic acid binding function given the proteins three-dimensional structure or a structural model. Additionally, BindUP provides information on the largest electrostatic surface patches, visualized on the server. The server was tested on several datasets of DNA and RNA binding proteins, including proteins which do not possess DNA or RNA binding domains and have no similarity to known nucleic acid binding proteins, achieving very high accuracy. BindUP is applicable in either single or batch modes and can be applied for testing hundreds of proteins simultaneously in a highly efficient manner.

  9. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole;

    2010-01-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.......0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models.......3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is...

  10. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Science.gov (United States)

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-08

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.

    Science.gov (United States)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl

    2010-07-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is web server is available at http://www.cbs.dtu.dk/services/CPHmodels/.

  12. Sequence analysis and homology modeling of laccase from Pycnoporus cinnabarinus.

    Science.gov (United States)

    Meshram, Rohan J; Gavhane, Aj; Gaikar, Rb; Bansode, Ts; Maskar, Au; Gupta, Ak; Sohni, Sk; Patidar, Ma; Pandey, Tr; Jangle, Sn

    2010-09-20

    Industrial effluents of textile, paper, and leather industries contain various toxic dyes as one of the waste material. It imparts major impact on human health as well as environment. The white rot fungus Pycnoporus cinnabarinus Laccase is generally used to degrade these toxic dyes. In order to decipher the mechanism of process by which Laccase degrade dyes, it is essential to know its 3D structure. Homology modeling was performed in presented work, by satisfying Spatial restrains using Modeller Program, which is considered as standard in this field, to generate 3D structure of Laccase in unison, SWISSMODEL web server was also utilized to generate and verify the alternative models. We observed that models created using Modeller stands better on structure evaluation tests. This study can further be used in molecular docking techniques, to understand the interaction of enzyme with its mediators like 2, 2-azinobis (3-ethylbenzthiazoline-6-sulfonate) (ABTS) and Vanillin that are known to enhance the Laccase activity.

  13. A CONFERENCE CONTROL MODEL BETWEEN A WEB SERVER AND A TELECOM APPLICATION SERVER

    Institute of Scientific and Technical Information of China (English)

    Wang Kaixi; Yang Fangchun

    2008-01-01

    The paper proposes a conference control model between a web server and a telecom application server, referred to as the Conference Directed Graph (CDG), and describes an asynchronous communication mechanism between them. The Corba Interface Definition Language (IDL) interfaces are defined, and a message sequence chart is illustrated. This web conference control model provides conference users with a new approach to manage and control a conference and the participants. The performance of the system prototype is analyzed and verified in the 863 project named "The Multimedia and Mobile Services Enabled Soft-switch System".

  14. Client Server Model Based DAQ System for Real-Time Air Pollution Monitoring

    Directory of Open Access Journals (Sweden)

    Vetrivel. P

    2014-01-01

    Full Text Available The proposed system consists of client server model based Data-Acquisition Unit. The Embedded Web Server integrates Pollution Server and DAQ that collects air Pollutants levels (CO, NO2, and SO2. The Pollution Server is designed by considering modern resource constrained embedded systems. In contrast, an application server is designed to the efficient execution of programs and scripts for supporting the construction of various applications. While a pollution server mainly deals with sending HTML for display in a web browser on the client terminal, an application server provides access to server side logic for pollutants levels to be use by client application programs. The Embedded Web Server is an arm mcb2300 board with internet connectivity and acts as air pollution server as this standalone device gathers air pollutants levels and as a Server. Embedded Web server is accessed by various clients.

  15. PENERAPAN PENGOLAHAN PARALEL MODEL CLUSTER SEBAGAI WEB SERVER

    Directory of Open Access Journals (Sweden)

    Maman Somantri

    2009-06-01

    Full Text Available engolahan paralel merupakan suatu cara yang dilakukan untuk meningkatkan kecepatan pengolahandata dengan melakukan lebih dari satu pengolahan data tersebut secara bersamaan. Salah satu bentuk pengolahanparalel adalah model cluster. Pengolahan paralel model cluster ini akan digunakan untuk mengolah data Web,dengan membangun server Web yang di-cluster. Cluster server Web ini menggunakan teknologi Linux VirtualServer (LVS yang dapat dilakukan dengan NAT, IP tunneling, dan direct routing yang memiliki empat algoritmapenjadwalan.Pada penelitian ini akan digunakan teknologi LVS untuk membuat cluster Web Server denganmenggunakan NAT, diterapkannya teknologi Network File System, dan Network Block Device yang digunakansebagai media penyimpanan dalam jaringan. Dalam pengujian sistem cluster ini, pertama dilakukan pengujianjaringan yang digunakan untuk mengetahui kinerja sistem, dan pengujian sistem cluster dalam mengolah data Webdengan perangkat lunak WebBench dan script benchmark.

  16. Dynamic server assignment in a two-queue model

    NARCIS (Netherlands)

    Boxma, O.J.; Down, D.G.

    1995-01-01

    We consider a polling model of two $M/G/1$ queues, served by a single server. The service policy for this polling model is of threshold type. Service at queue 1 is exhaustive. Service at queue 2 is exhaustive unless the size of queue 1 reaches some level $T$ during a service at queue 2; in the latte

  17. Parmodel: a web server for automated comparative modeling of proteins.

    Science.gov (United States)

    Uchôa, Hugo Brandão; Jorge, Guilherme Eberhart; Freitas Da Silveira, Nelson José; Camera, João Carlos; Canduri, Fernanda; De Azevedo, Walter Filgueira

    2004-12-24

    Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at .

  18. Note on homological modeling of the electric circuits

    OpenAIRE

    2014-01-01

    Based on a simple example, it is explained how the homological analysis may be applied for modeling of the electric circuits. The homological branch, mesh and nodal analyses are presented. Geometrical interpretations are given.

  19. Modeling Non-homologous End Joining

    Science.gov (United States)

    Li, Yongfeng

    2013-01-01

    Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

  20. Excluded volume effect enhances the homology pairing of model chromosomes

    CERN Document Server

    Takamiya, Kazunori; Isami, Shuhei; Nishimori, Hiraku; Awazu, Akinori

    2015-01-01

    To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We consider a simple model consist- ing of pairs of homologous polymers with the same structures that are confined in a cylindrical container, which represents the local parts of chromosomes contained in an elongated nucleus of S. pombe. Brownian dynamics simulations of this model showed that the excluded volume effects among non-homological chromosomes and the transitional dynamics of nuclear shape serve to enhance the pairing of homologous chromosomes.

  1. Excluded volume effect enhances the homology pairing of model chromosomes

    Science.gov (United States)

    Takamiya, Kazunori; Yamamoto, Keisuke; Isami, Shuhei; Nishimori, Hiraku; Awazu, Akinori

    To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We consider a simple model consist- ing of pairs of homologous polymers with the same structures that are confined in a cylindrical container, which represents the local parts of chromosomes contained in an elongated nucleus of S. pombe. Brownian dynamics simulations of this model showed that the excluded volume effects among non-homological chromosomes and the transitional dynamics of nuclear shape serve to enhance the pairing of homologous chromosomes.

  2. 3D-DART: a DNA structure modelling server

    NARCIS (Netherlands)

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

    2009-01-01

    There is a growing interest in structural studies of DNA by both experimental and computational approaches. Often, 3D-structural models of DNA are required, for instance, to serve as templates for homology modeling, as starting structures for macro-molecular docking or as scaffold for NMR structure

  3. Remarks on Khovanov Homology and the Potts Model

    CERN Document Server

    Kauffman, Louis H

    2009-01-01

    This paper is about Khovanov homology and its relationships with statistical mechanics models such as the Ising model and the Potts model. The paper gives a relatively self-contained introduction to Khovanov homology, and also to a reformulation of the Potts model in terms of a bracket state sum expansion on a knot diagram K(G) related to a planar graph G via the medial construction. We consider the original Khovanov homology and also the homology defined by Stosic via the dichromatic polynomial, and examine those values of the Potts model where the partition function can be expressed in terms of homological Euler characteristics. These points occur at imaginary temperature, and consequences of this phenomenon will be studied in subsequent work. This paper is dedicated to Oleg Viro on his 60-th birthday.

  4. HLA-Modeler: Automated Homology Modeling of Human Leukocyte Antigens

    Directory of Open Access Journals (Sweden)

    Shinji Amari

    2013-01-01

    Full Text Available The three-dimensional (3D structures of human leukocyte antigen (HLA molecules are indispensable for the studies on the functions at molecular level. We have developed a homology modeling system named HLA-modeler specialized in the HLA molecules. Segment matching algorithm is employed for modeling and the optimization of the model is carried out by use of the PFROSST force field considering the implicit solvent model. In order to efficiently construct the homology models, HLA-modeler uses a local database of the 3D structures of HLA molecules. The structure of the antigenic peptide-binding site is important for the function and the 3D structure is highly conserved between various alleles. HLA-modeler optimizes the use of this structural motif. The leave-one-out cross-validation using the crystal structures of class I and class II HLA molecules has demonstrated that the rmsds of nonhydrogen atoms of the sites between homology models and crystal structures are less than 1.0 Å in most cases. The results have indicated that the 3D structures of the antigenic peptide-binding sites can be reproduced by HLA-modeler at the level almost corresponding to the crystal structures.

  5. HLA-Modeler: Automated Homology Modeling of Human Leukocyte Antigens.

    Science.gov (United States)

    Amari, Shinji; Kataoka, Ryoichi; Ikegami, Takashi; Hirayama, Noriaki

    2013-01-01

    The three-dimensional (3D) structures of human leukocyte antigen (HLA) molecules are indispensable for the studies on the functions at molecular level. We have developed a homology modeling system named HLA-modeler specialized in the HLA molecules. Segment matching algorithm is employed for modeling and the optimization of the model is carried out by use of the PFROSST force field considering the implicit solvent model. In order to efficiently construct the homology models, HLA-modeler uses a local database of the 3D structures of HLA molecules. The structure of the antigenic peptide-binding site is important for the function and the 3D structure is highly conserved between various alleles. HLA-modeler optimizes the use of this structural motif. The leave-one-out cross-validation using the crystal structures of class I and class II HLA molecules has demonstrated that the rmsds of nonhydrogen atoms of the sites between homology models and crystal structures are less than 1.0 Å in most cases. The results have indicated that the 3D structures of the antigenic peptide-binding sites can be reproduced by HLA-modeler at the level almost corresponding to the crystal structures.

  6. SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins.

    Science.gov (United States)

    Hildebrand, Peter W; Goede, Andrean; Bauer, Raphael A; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preissner, Robert

    2009-07-01

    SuperLooper provides the first online interface for the automatic, quick and interactive search and placement of loops in proteins (LIP). A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops. A specified database containing 180,000 membrane loops in proteins (LIMP) can be searched, alternatively. Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms. Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 A, for loops up to six residues or <3 A for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, the sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted. For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/.

  7. SuperLooper—a prediction server for the modeling of loops in globular and membrane proteins

    Science.gov (United States)

    Hildebrand, Peter W.; Goede, Andrean; Bauer, Raphael A.; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preissner, Robert

    2009-01-01

    SuperLooper provides the first online interface for the automatic, quick and interactive search and placement of loops in proteins (LIP). A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops. A specified database containing 180 000 membrane loops in proteins (LIMP) can be searched, alternatively. Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms. Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 Å, for loops up to six residues or <3 Å for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, the sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted. For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/ PMID:19429894

  8. A geometric model for Hochschild homology of Soergel bimodules

    DEFF Research Database (Denmark)

    Webster, Ben; Williamson, Geordie

    2008-01-01

    An important step in the calculation of the triply graded link homology of Khovanov and Rozansky is the determination of the Hochschild homology of Soergel bimodules for SL(n). We present a geometric model for this Hochschild homology for any simple group G, as B–equivariant intersection cohomology...... of B×B–orbit closures in G. We show that, in type A, these orbit closures are equivariantly formal for the conjugation B–action. We use this fact to show that, in the case where the corresponding orbit closure is smooth, this Hochschild homology is an exterior algebra over a polynomial ring...

  9. Analysis of a multi-server queueing model of ABR

    Directory of Open Access Journals (Sweden)

    R. Núñez-Queija

    1998-01-01

    Full Text Available In this paper we present a queueing model for the performance analysis of Available Bit Rate (ABR traffic in Asynchronous Transfer Mode (ATM networks. We consider a multi-channel service station with two types of customers, denoted by high priority and low priority customers. In principle, high priority customers have preemptive priority over low priority customers, except on a fixed number of channels that are reserved for low priority traffic. The arrivals occur according to two independent Poisson processes, and service times are assumed to be exponentially distributed. Each high priority customer requires a single server, whereas low priority customers are served in processor sharing fashion. We derive the joint distribution of the numbers of customers (of both types in the system in steady state. Numerical results illustrate the effect of high priority traffic on the service performance of low priority traffic.

  10. Creating A Model HTTP Server Program Using java

    CERN Document Server

    Veerasamy, Bala Dhandayuthapani

    2010-01-01

    HTTP Server is a computer programs that serves webpage content to clients. A webpage is a document or resource of information that is suitable for the World Wide Web and can be accessed through a web browser and displayed on a computer screen. This information is usually in HTML format, and may provide navigation to other webpage's via hypertext links. WebPages may be retrieved from a local computer or from a remote HTTP Server. WebPages are requested and served from HTTP Servers using Hypertext Transfer Protocol (HTTP). WebPages may consist of files of static or dynamic text stored within the HTTP Server's file system. Client-side scripting can make WebPages more responsive to user input once in the client browser. This paper encompasses the creation of HTTP server program using java language, which is basically supporting for HTML and JavaScript.

  11. Real-Time Robust Adaptive Modeling and Scheduling for an Electronic Commerce Server

    Science.gov (United States)

    Du, Bing; Ruan, Chun

    With the increasing importance and pervasiveness of Internet services, it is becoming a challenge for the proliferation of electronic commerce services to provide performance guarantees under extreme overload. This paper describes a real-time optimization modeling and scheduling approach for performance guarantee of electronic commerce servers. We show that an electronic commerce server may be simulated as a multi-tank system. A robust adaptive server model is subject to unknown additive load disturbances and uncertain model matching. Overload control techniques are based on adaptive admission control to achieve timing guarantees. We evaluate the performance of the model using a complex simulation that is subjected to varying model parameters and massive overload.

  12. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

    Science.gov (United States)

    Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg, Miquel; Montanyola, Alberto; Chang, Jia-Ming; Taly, Jean-François; Notredame, Cedric

    2011-07-01

    This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

  13. Multiple Servers - Queue Model for Agent Based Technology in Cache Consistence Maintenance of Mobile Environment

    Directory of Open Access Journals (Sweden)

    G.Shanmugarathinam

    2013-01-01

    Full Text Available Caching is one of the important techniques in mobile computing. In caching, frequently accessed data is stored in mobile clients to avoid network traffic and improve the performance in mobile computing. In a mobile computing environment, the number of mobile users increases and requests the server for any updation, but most of the time the server is busy and the client has to wait for a long time. The cache consistency maintenance is difficult for both client and the server. This paper is proposes a technique using a queuing system consisting of one or more servers that provide services of some sort to arrive mobile hosts using agent based technology. This services mechanism of a queuing system is specified by the number of servers each server having its own queue, Agent based technology will maintain the cache consistency between the client and the server .This model saves wireless bandwidth, reduces network traffic and reduces the workload on the server. The simulation result was analyzed with previous technique and the proposed model shows significantly better performance than the earlier approach.

  14. Structural insights into a high affinity nanobody:antigen complex by homology modelling

    DEFF Research Database (Denmark)

    Skottrup, Peter Durand

    2017-01-01

    B binding were identified and used as input to the docking. Furthermore, residues likely involved in the RgpB epitope was identified based upon RgpB:RgpA alignment and analysis of residue surface accessibility. CDR residues and putitative RgpB epitope residues were used as input to an information-driven...... flexible docking approach using the HADDOCK server. Analysis of the VHH7:RgpB model demonstrated that the epitope was found in the immunoglobulin-like domain and residue pairs located at the molecular paratope:epitope interface important for complex stability was identified. Collectively, the VHH7 homology...... model and VHH7:RgpB docking supplies knowledge of the residues involved in the high affinity interaction. This information could prove valuable in the design of an antibody-drug conjugate for specific RgpB targeting....

  15. Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives

    Science.gov (United States)

    Vyas, V. K.; Ukawala, R. D.; Ghate, M.; Chintha, C.

    2012-01-01

    Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery. PMID:23204616

  16. Many-server queues with customer abandonment: Numerical analysis of their diffusion model

    Directory of Open Access Journals (Sweden)

    Shuangchi He

    2013-01-01

    Full Text Available We use a multidimensional diffusion process to approximate the dynamics of aqueue served by many parallel servers. Waiting customers in this queue may abandonthe system without service. To analyze the diffusion model, we develop a numericalalgorithm for computing its stationary distribution. A crucial part of the algorithm ischoosing an appropriate reference density. Using a conjecture on the tailbehavior of the limit queue length process, we propose a systematic approach toconstructing a reference density. With the proposed reference density, thealgorithm is shown to converge quickly in numerical experiments. Theseexperiments demonstrate that the diffusion model is a satisfactory approximation formany-server queues, sometimes for queues with as few as twenty servers.

  17. RNA Structural Homology Search with a Succinct Stochastic Grammar Model

    Institute of Scientific and Technical Information of China (English)

    Ying-Lei Song; Ji-Zhen Zhao; Chun-Mei Liu; Kan Liu; Russell Malmberg; Li-Ming Cai

    2005-01-01

    An increasing number of structural homology search tools, mostly based on profile stochastic context-free grammars (SCFGs) have been recently developed for the non-coding RNA gene identification. SCFGs can include statistical biases that often occur in RNA sequences, necessary to profile specific RNA structures for structural homology search. In this paper, a succinct stochastic grammar model is introduced for RNA that has competitive search effectiveness. More importantly, the profiling model can be easily extended to include pseudoknots, structures that are beyond the capability of profile SCFGs. In addition, the model allows heuristics to be exploited, resulting in a significant speed-up for the CYK algorithm-based search.

  18. Homology modeling: an important tool for the drug discovery.

    Science.gov (United States)

    França, Tanos Celmar Costa

    2015-01-01

    In the last decades, homology modeling has become a popular tool to access theoretical three-dimensional (3D) structures of molecular targets. So far several 3D models of proteins have been built by this technique and used in a great diversity of structural biology studies. But are those models consistent enough with experimental structures to make this technique an effective and reliable tool for drug discovery? Here we present, briefly, the fundamentals and current state-of-the-art of the homology modeling techniques used to build 3D structures of molecular targets, which experimental structures are not available in databases, and list some of the more important works, using this technique, available in literature today. In many cases those studies have afforded successful models for the drug design of more selective agonists/antagonists to the molecular targets in focus and guided promising experimental works, proving that, when the appropriate templates are available, useful models can be built using some of the several software available today for this purpose. Limitations of the experimental techniques used to solve 3D structures allied to constant improvements in the homology modeling software will maintain the need for theoretical models, establishing the homology modeling as a fundamental tool for the drug discovery.

  19. Performance model of the Argonne Voyager multimedia server

    Energy Technology Data Exchange (ETDEWEB)

    Disz, T.; Olson, R.; Stevens, R. [Argonne National Lab., IL (United States). Mathematics and Computer Science Div.

    1997-07-01

    The Argonne Voyager Multimedia Server is being developed in the Futures Lab of the Mathematics and Computer Science Division at Argonne National Laboratory. As a network-based service for recording and playing multimedia streams, it is important that the Voyager system be capable of sustaining certain minimal levels of performance in order for it to be a viable system. In this article, the authors examine the performance characteristics of the server. As they examine the architecture of the system, they try to determine where bottlenecks lie, show actual vs potential performance, and recommend areas for improvement through custom architectures and system tuning.

  20. Illustrating and homology modeling the proteins of the Zika virus

    Science.gov (United States)

    Ekins, Sean; Liebler, John; Neves, Bruno J.; Lewis, Warren G.; Coffee, Megan; Bienstock, Rachelle; Southan, Christopher; Andrade, Carolina H.

    2016-01-01

    The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening. PMID:27746901

  1. Illustrating and homology modeling the proteins of the Zika virus.

    Science.gov (United States)

    Ekins, Sean; Liebler, John; Neves, Bruno J; Lewis, Warren G; Coffee, Megan; Bienstock, Rachelle; Southan, Christopher; Andrade, Carolina H

    2016-01-01

    The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

  2. Application Server Aging Model and Multi-Level Rejuvenation Strategy Using Semi-Markov Process

    Institute of Scientific and Technical Information of China (English)

    ZHAO Tianhai; QI Yong; SHEN Junyi; HOU Di; ZHENG Xiaomei; LIU Liang

    2006-01-01

    Aiming at the characteristic of the dependency between the application components and the application server platform, a rejuvenation strategy with two different levels of rejuvenation granularities is put forward in this paper including the application component rejuvenation and the application server system rejuvenation. The availability and maintenance cost functions are obtained by means of establishing the application server aging model and the boundary condition of the optimal rejuvenation time is analyzed. Theory analysis indicates that the two-level rejuvenation strategy is superior to the traditional single level one. Finally, evaluation experiments are carried out and numerical result shows that compared with the traditional rejuvenation policy, the rejuvenation strategy proposed in this paper can further increase availability of the application server and reduce maintenance cost.

  3. Guidelines for Homology Modeling of Dopamine, Norepinephrine, and Serotonin Transporters.

    Science.gov (United States)

    Haddad, Yazan; Heger, Zbynek; Adam, Vojtech

    2016-11-16

    The human dopamine, norepinephrine, and serotonin transporters (hDAT, hNET, and hSERT) are carriers of neurotransmitters and targets for many drugs. Pioneering works in the past three years to elucidate experimental models of the Drosophila dDAT and human hSERT structures will rapidly impact the field of neuroscience. Here, we evaluated automated homology-based human models of these transporters, employing systematic physics-based, knowledge-based, and empirical-based check. Modeling guidelines were conveyed with attention to the central binding site (S1), secondary binding site (S2), and the extracellular loops EL2 and EL4. Application of new experimental models (dDAT and hSERT) will improve the accuracy of homology models, previously utilizing prokaryotic leucine transporter (LeuT) structure, and provide better predictions of ligand interactions, which is required for understanding of cellular mechanisms and for development of novel therapeutics.

  4. RaptorX-Property: a web server for protein structure property prediction

    OpenAIRE

    Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

    2016-01-01

    RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent acce...

  5. A novel homologous model for noninvasive monitoring of endometriosis progression.

    Science.gov (United States)

    Ferrero, Hortensia; Buigues, Anna; Martínez, Jessica; Simón, Carlos; Pellicer, Antonio; Gómez, Raúl

    2017-02-01

    To date, several groups have generated homologous models of endometriosis through the implantation of endometrial tissue fluorescently labeled by green fluorescent protein (GFP) or tissue from luciferase-expressing transgenic mice into recipient animals, enabling noninvasive monitoring of lesion signal. These models present an advantage over endpoint models, but some limitations persist; use of transgenic mice is laborious and expensive, and GFP presents poor tissue penetration due to the relatively short emission wavelength. For this reason, a homologous mouse model of endometriosis that allows in vivo monitoring of generated lesions over time and mimics human lesions in recipient mice would be most desirable. In this regard, using C57BL/6 and B6N-Tyrc-Brd/BrdCrCrl mice, we optimized a decidualization protocol to obtain large volumes of decidual endometrium and mimic human lesions. Subsequently, to obtain a more robust and reliable noninvasive monitoring of lesions, we used the fluorescent reporter mCherry, which presents deeper tissue penetration and higher photostability, showing that endometrial tissue was properly labeled with 1 × 108 PFU/mL mCherry adenoviral vectors. mCherry-labeled endometriotic tissue was implanted in recipient mice, generating lesions that displayed characteristics typical of human endometriotic lesions, such as epithelial cells forming glands, local inflammation, collagen deposits, and new vessel formation. In vivo monitoring demonstrated that subcutaneous implantation on ventral abdomen of recipient mice provided the most intense and reliable signal for noninvasive lesion monitoring over a period of at least 20 days. This homologous model improves upon previously reported models of endometriosis and provides opportunities to study mechanism underlying endometriotic lesion growth and progression. We created a cost-effective but accurate homologous mouse model of endometriosis that allows the study of growth and progression of

  6. Three-Dimensional Modeling of Quasi-Homologous Solar Jets

    Science.gov (United States)

    Pariat, E.; Antiochos, S. K.; DeVore, C. R.

    2010-01-01

    Recent solar observations (e.g., obtained with Hinode and STEREO) have revealed that coronal jets are a more frequent phenomenon than previously believed. This higher frequency results, in part, from the fact that jets exhibit a homologous behavior: successive jets recur at the same location with similar morphological features. We present the results of three-dimensional (31)) numerical simulations of our model for coronal jets. This study demonstrates the ability of the model to generate recurrent 3D untwisting quasi-homologous jets when a stress is constantly applied at the photospheric boundary. The homology results from the property of the 3D null-point system to relax to a state topologically similar to its initial configuration. In addition, we find two distinct regimes of reconnection in the simulations: an impulsive 3D mode involving a helical rotating current sheet that generates the jet, and a quasi-steady mode that occurs in a 2D-like current sheet located along the fan between the sheared spines. We argue that these different regimes can explain the observed link between jets and plumes.

  7. A Case Study of Employing A Single Server Nonpreemptive Priority Queuing Model at ATM Machine

    OpenAIRE

    Abdullah Furquan; Abdullah Imran

    2015-01-01

    This paper discusses a case study of employing a single server nonpreemptivepriorityqueuing model [1]at ATM machine which originally operates on M/M/1 model. In this study we have taken two priority classes of people in following order:- .Priority class 1- woman .Priority class 2- man Sometimea long queue is formed at ATMmachine (single server)but the bank management don’t have enough money to invest on installing new ATM machine.In this situation we want to apply single ser...

  8. In silico Sequence Analysis, Homology Modeling and Function Annotation of Ocimum basilicum Hypothetical Protein G1CT28_OCIBA

    Directory of Open Access Journals (Sweden)

    Sobia Idrees

    2012-07-01

    Full Text Available Ocimum basilicum is commonly known as sweet basil and belongs to the Lamiaceae Family. Ocimum basilicum has great therapeutic benefits and can be used for lowering blood pressure, as an antispasmodic as well as cleansing the blood. In the present study, subcellular localization prediction suggested that it is a cytoplasmic protein. We predicted the 3D structure of protein using homology modeling as 3D structure prediction approach. 3D structure of the protein was determined using Protein Structure Prediction Server (PS2 selecting MODELLER as 3D structure prediction method. Quality analysis of the model indicated that it is a reliable model. Furthermore, it was discovered that Ocimum basilicum hypothetical protein G1CT28_OCIBA is involved in two biological processes, oxidation reduction and metabolic process and the biochemical function of the protein is acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, catalytic activity and oxidoreductase.

  9. Relative Binding Free Energy Calculations Applied to Protein Homology Models.

    Science.gov (United States)

    Cappel, Daniel; Hall, Michelle Lynn; Lenselink, Eelke B; Beuming, Thijs; Qi, Jun; Bradner, James; Sherman, Woody

    2016-12-27

    A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points-something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein-protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the "real" conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with

  10. A quality metric for homology modeling: the H-factor

    Science.gov (United States)

    2011-01-01

    Background The analysis of protein structures provides fundamental insight into most biochemical functions and consequently into the cause and possible treatment of diseases. As the structures of most known proteins cannot be solved experimentally for technical or sometimes simply for time constraints, in silico protein structure prediction is expected to step in and generate a more complete picture of the protein structure universe. Molecular modeling of protein structures is a fast growing field and tremendous works have been done since the publication of the very first model. The growth of modeling techniques and more specifically of those that rely on the existing experimental knowledge of protein structures is intimately linked to the developments of high resolution, experimental techniques such as NMR, X-ray crystallography and electron microscopy. This strong connection between experimental and in silico methods is however not devoid of criticisms and concerns among modelers as well as among experimentalists. Results In this paper, we focus on homology-modeling and more specifically, we review how it is perceived by the structural biology community and what can be done to impress on the experimentalists that it can be a valuable resource to them. We review the common practices and provide a set of guidelines for building better models. For that purpose, we introduce the H-factor, a new indicator for assessing the quality of homology models, mimicking the R-factor in X-ray crystallography. The methods for computing the H-factor is fully described and validated on a series of test cases. Conclusions We have developed a web service for computing the H-factor for models of a protein structure. This service is freely accessible at http://koehllab.genomecenter.ucdavis.edu/toolkit/h-factor. PMID:21291572

  11. A More Complete Model for TCP Connections Established between One Server and Many Receivers

    Institute of Scientific and Technical Information of China (English)

    LINYu; CHENGShiduan; WUHaitao; WANGChonggang

    2003-01-01

    Different from previous TCP (transmis-sion control program) modeling works, this paper presents a more complete analytical model of multiple TCP con-nections established between a busy server and multiple receivers under two distinct cases: the case there is suffi-cient bandwidth and the case there is a bandwidth bottle-neck link between the server and receivers. In the former case, the server will become the bottleneck of the whole system, and TCP behaviors are different from the model presented before. However, in the latter case, multiple TCP connections will share the bandwidth of the bottle-neck link. Based on the analysis of working flows in the system and a M/G/1 queueing model, the RTT and long-term TCP throughput formulae are derived in terms of number of TCPs, packet loss rate, and end-to-end delay.And the effect of maximum window size is also investi-gated. The simulation results confirm that new model is more accurate than previous model.

  12. Refined homology model of monoacylglycerol lipase: toward a selective inhibitor

    Science.gov (United States)

    Bowman, Anna L.; Makriyannis, Alexandros

    2009-11-01

    Monoacylglycerol lipase (MGL) is primarily responsible for the hydrolysis of 2-arachidonoylglycerol (2-AG), an endocannabinoid with full agonist activity at both cannabinoid receptors. Increased tissue 2-AG levels consequent to MGL inhibition are considered therapeutic against pain, inflammation, and neurodegenerative disorders. However, the lack of MGL structural information has hindered the development of MGL-selective inhibitors. Here, we detail a fully refined homology model of MGL which preferentially identifies MGL inhibitors over druglike noninhibitors. We include for the first time insight into the active-site geometry and potential hydrogen-bonding interactions along with molecular dynamics simulations describing the opening and closing of the MGL helical-domain lid. Docked poses of both the natural substrate and known inhibitors are detailed. A comparison of the MGL active-site to that of the other principal endocannabinoid metabolizing enzyme, fatty acid amide hydrolase, demonstrates key differences which provide crucial insight toward the design of selective MGL inhibitors as potential drugs.

  13. From honeybees to Internet servers: biomimicry for distributed management of Internet hosting centers.

    Science.gov (United States)

    Nakrani, Sunil; Tovey, Craig

    2007-12-01

    An Internet hosting center hosts services on its server ensemble. The center must allocate servers dynamically amongst services to maximize revenue earned from hosting fees. The finite server ensemble, unpredictable request arrival behavior and server reallocation cost make server allocation optimization difficult. Server allocation closely resembles honeybee forager allocation amongst flower patches to optimize nectar influx. The resemblance inspires a honeybee biomimetic algorithm. This paper describes details of the honeybee self-organizing model in terms of information flow and feedback, analyzes the homology between the two problems and derives the resulting biomimetic algorithm for hosting centers. The algorithm is assessed for effectiveness and adaptiveness by comparative testing against benchmark and conventional algorithms. Computational results indicate that the new algorithm is highly adaptive to widely varying external environments and quite competitive against benchmark assessment algorithms. Other swarm intelligence applications are briefly surveyed, and some general speculations are offered regarding their various degrees of success.

  14. Disk Storage Server

    CERN Multimedia

    This model was a disk storage server used in the Data Centre up until 2012. Each tray contains a hard disk drive (see the 5TB hard disk drive on the main disk display section - this actually fits into one of the trays). There are 16 trays in all per server. There are hundreds of these servers mounted on racks in the Data Centre, as can be seen.

  15. A Case Study of Employing A Single Server Nonpreemptive Priority Queuing Model at ATM Machine

    Directory of Open Access Journals (Sweden)

    Abdullah Furquan

    2015-08-01

    Full Text Available This paper discusses a case study of employing a single server nonpreemptivepriorityqueuing model [1]at ATM machine which originally operates on M/M/1 model. In this study we have taken two priority classes of people in following order:- .Priority class 1- woman .Priority class 2- man Sometimea long queue is formed at ATMmachine (single serverbut the bank management don’t have enough money to invest on installing new ATM machine.In this situation we want to apply single server nonpreemptive priority queuing model.The security guard at the ATM will divide the customers in two category and arrange the customers in the above said priority order Thuspriority class 1 people willreceive theatm service ahead of priority class 2 people.This will reduce the waiting time of priority class 1 people. Of course by doing this the waiting time of priority class 2will increase. This is ok as long as the increment in waiting time of priority class2 people is reasonable and within the tolerable limitof priority class 2people.This will be true when percentage of priority class 1 people is relatively less as compared to priority class 2 people To know the attitude and tolerable limit of priority class 2 people towards the single server non preemtive priority model a sample survey has been done on the incomingpriority class 2 population at the atm machine.Against this background, the queuing process is employed with emphasis to Poisson distribution to assess the waiting time. The data for this study was collected from primary source and is limited to ATM service point of state bank of India located at Ramesh chowk, Aurangabad, bihar, India.. The assistance of three colleague was sought in collecting the data. The Interarrival time and service time data was collected during busy working hours (i.e. 10.30am to 4:00pm during the first 60 days. A sample survey was done to know the attitude and tolerable limit of priority class 2people towards the single server

  16. A new model for virtual machine migration in virtualized cluster server based on Fuzzy Decision Making

    CERN Document Server

    Tarighi, M; Sharifian, S

    2010-01-01

    In this paper, we show that performance of the virtualized cluster servers could be improved through intelligent decision over migration time of Virtual Machines across heterogeneous physical nodes of a cluster server. The cluster serves a variety range of services from Web Service to File Service. Some of them are CPU-Intensive while others are RAM-Intensive and so on. Virtualization has many advantages such as less hardware cost, cooling cost, more manageability. One of the key benefits is better load balancing by using of VM migration between hosts. To migrate, we must know which virtual machine needs to be migrated and when this relocation has to be done and, moreover, which host must be destined. To relocate VMs from overloaded servers to underloaded ones, we need to sort nodes from the highest volume to the lowest. There are some models to finding the most overloaded node, but they have some shortcomings. The focus of this paper is to present a new method to migrate VMs between cluster nodes using TOPSI...

  17. A Comprehensive Availability Modeling and Analysis of a Virtualized Servers System Using Stochastic Reward Nets

    Directory of Open Access Journals (Sweden)

    Tuan Anh Nguyen

    2014-01-01

    Full Text Available It is important to assess availability of virtualized systems in IT business infrastructures. Previous work on availability modeling and analysis of the virtualized systems used a simplified configuration and assumption in which only one virtual machine (VM runs on a virtual machine monitor (VMM hosted on a physical server. In this paper, we show a comprehensive availability model using stochastic reward nets (SRN. The model takes into account (i the detailed failures and recovery behaviors of multiple VMs, (ii various other failure modes and corresponding recovery behaviors (e.g., hardware faults, failure and recovery due to Mandelbugs and aging-related bugs, and (iii dependency between different subcomponents (e.g., between physical host failure and VMM, etc. in a virtualized servers system. We also show numerical analysis on steady state availability, downtime in hours per year, transaction loss, and sensitivity analysis. This model provides a new finding on how to increase system availability by combining both software rejuvenations at VM and VMM in a wise manner.

  18. Structural analysis of diheme cytochrome c by hydrogen-deuterium exchange mass spectrometry and homology modeling.

    Science.gov (United States)

    Zhang, Ying; Majumder, Erica L-W; Yue, Hai; Blankenship, Robert E; Gross, Michael L

    2014-09-09

    A lack of X-ray or nuclear magnetic resonance structures of proteins inhibits their further study and characterization, motivating the development of new ways of analyzing structural information without crystal structures. The combination of hydrogen-deuterium exchange mass spectrometry (HDX-MS) data in conjunction with homology modeling can provide improved structure and mechanistic predictions. Here a unique diheme cytochrome c (DHCC) protein from Heliobacterium modesticaldum is studied with both HDX and homology modeling to bring some definition of the structure of the protein and its role. Specifically, HDX data were used to guide the homology modeling to yield a more functionally relevant structural model of DHCC.

  19. Critical analysis of the successes and failures of homology models of G protein-coupled receptors.

    Science.gov (United States)

    Bhattacharya, Supriyo; Lam, Alfonso Ramon; Li, Hubert; Balaraman, Gouthaman; Niesen, Michiel Jacobus Maria; Vaidehi, Nagarajan

    2013-05-01

    We present a critical assessment of the performance of our homology model refinement method for G protein-coupled receptors (GPCRs), called LITICon that led to top ranking structures in a recent structure prediction assessment GPCRDOCK2010. GPCRs form the largest class of drug targets for which only a few crystal structures are currently available. Therefore, accurate homology models are essential for drug design in these receptors. We submitted five models each for human chemokine CXCR4 (bound to small molecule IT1t and peptide CVX15) and dopamine D3DR (bound to small molecule eticlopride) before the crystal structures were published. Our models in both CXCR4/IT1t and D3/eticlopride assessments were ranked first and second, respectively, by ligand RMSD to the crystal structures. For both receptors, we developed two types of protein models: homology models based on known GPCR crystal structures, and ab initio models based on the prediction method MembStruk. The homology-based models compared better to the crystal structures than the ab initio models. However, a robust refinement procedure for obtaining high accuracy structures is needed. We demonstrate that optimization of the helical tilt, rotation, and translation is vital for GPCR homology model refinement. As a proof of concept, our in-house refinement program LITiCon captured the distinct orientation of TM2 in CXCR4, which differs from that of adrenoreceptors. These findings would be critical for refining GPCR homology models in future. Copyright © 2012 Wiley Periodicals, Inc.

  20. Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling.

    Science.gov (United States)

    Lupala, Cecylia S; Rasaeifar, Bahareh; Gomez-Gutierrez, Patricia; Perez, Juan J

    2017-08-14

    Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.

  1. Analisis Arsitektur Aplikasi Web Menggunakan Model View Controller (MVC pada Framework Java Server Faces

    Directory of Open Access Journals (Sweden)

    Gunawan Gunawan

    2016-06-01

    Full Text Available Aplikasi web yang khususnya memiliki kompleksitas besar dalam melakukan transaksi data sehingga konsep arsitektur (pattern perlu menjadi perhatian khusus untuk dapat mengoptimalkan kinerja performansi sistem ketika pengguna (user menggunakan dalam waktu yang bersamaan dengan jumlah yang banyak. Analisis performa arsitektur aplikasi web yang menggunakan model 2 (MVC dengan menggunakan framework Java Server Faces (JSF dan model 1 sebagai pembanding. Metode yang digunakan adalah Load dan Scalability Testing dengan dua cara yaitu uji coba terhadap response time karena peningkatan ukuran dari database dan uji coba terhadap response time karena peningkatan jumlah user yang menggunakan sistem secara bersamaan (concurrent users dan waktu tunggu (ramp-up yang ditentukan menggunakan Apache Jmeter. Analisis menunjukkan bahwa dalam implementasi arsitektur web yang menggunakan model 1 waktu rata-rata yang dibutuhkan untuk merespon permintaan user lebih cepat dan efisien dibanding model 2 (MVC.  

  2. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics

    Science.gov (United States)

    Petrovic, Dus?an; Zlatovic´, Mario

    2015-01-01

    A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL…

  3. Modeling Human Serum Albumin Tertiary Structure to Teach Upper-Division Chemistry Students Bioinformatics and Homology Modeling Basics

    Science.gov (United States)

    Petrovic, Dus?an; Zlatovic´, Mario

    2015-01-01

    A homology modeling laboratory experiment has been developed for an introductory molecular modeling course for upper-division undergraduate chemistry students. With this experiment, students gain practical experience in homology model preparation and assessment as well as in protein visualization using the educational version of PyMOL…

  4. A pluralistic account of homology: adapting the models to the data.

    Science.gov (United States)

    Haggerty, Leanne S; Jachiet, Pierre-Alain; Hanage, William P; Fitzpatrick, David A; Lopez, Philippe; O'Connell, Mary J; Pisani, Davide; Wilkinson, Mark; Bapteste, Eric; McInerney, James O

    2014-03-01

    Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as "public goods," subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define "family resemblances" to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet

  5. Gclust Server: [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 101823 Ava_Ava_1386 Cluster Sequences - 734 Lipopolysaccharide biosynthesis 1 1.00e...+00 0.0 0.0 4.0 0.0 0.0 0.0 Show 101823 Cluster ID 101823 Sequence ID Ava_Ava_1386 Link to cluster sequences Clus...ide biosynthesis Number of Sequences 1 Homologs 1 Clustering threshold 1.00e+00 P...each species Ava: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0

  6. A satellite-driven, client-server hydro-economic model prototype for agricultural water management

    Science.gov (United States)

    Maneta, Marco; Kimball, John; He, Mingzhu; Payton Gardner, W.

    2017-04-01

    Anticipating agricultural water demand, land reallocation, and impact on farm revenues associated with different policy or climate constraints is a challenge for water managers and for policy makers. While current integrated decision support systems based on programming methods provide estimates of farmer reaction to external constraints, they have important shortcomings such as the high cost of data collection surveys necessary to calibrate the model, biases associated with inadequate farm sampling, infrequent model updates and recalibration, model overfitting, or their deterministic nature, among other problems. In addition, the administration of water supplies and the generation of policies that promote sustainable agricultural regions depend on more than one bureau or office. Unfortunately, managers from local and regional agencies often use different datasets of variable quality, which complicates coordinated action. To overcome these limitations, we present a client-server, integrated hydro-economic modeling and observation framework driven by satellite remote sensing and other ancillary information from regional monitoring networks. The core of the framework is a stochastic data assimilation system that sequentially ingests remote sensing observations and corrects the parameters of the hydro-economic model at unprecedented spatial and temporal resolutions. An economic model of agricultural production, based on mathematical programming, requires information on crop type and extent, crop yield, crop transpiration and irrigation technology. A regional hydro-climatologic model provides biophysical constraints to an economic model of agricultural production with a level of detail that permits the study of the spatial impact of large- and small-scale water use decisions. Crop type and extent is obtained from the Cropland Data Layer (CDL), which is multi-sensor operational classification of crops maintained by the United States Department of Agriculture. Because

  7. Gclust Server: 107675 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available hatase PTEN (Phosphatase and tensin homolog) (Mutated in multiple advanced cancers 1) ; no annotation 1 9.98... tensin homolog) (Mutated in multiple advanced cancers 1) ; no annotation Number of Sequences 1 Homologs 1 C

  8. A Two-Tiered Model for Analyzing Library Web Site Usage Statistics, Part 1: Web Server Logs.

    Science.gov (United States)

    Cohen, Laura B.

    2003-01-01

    Proposes a two-tiered model for analyzing web site usage statistics for academic libraries: one tier for library administrators that analyzes measures indicating library use, and a second tier for web site managers that analyzes measures aiding in server maintenance and site design. Discusses the technology of web site usage statistics, and…

  9. Homology modeling of the CheW coupling protein of the chemotaxis signaling complex.

    Science.gov (United States)

    Cashman, Derek J; Ortega, Davi R; Zhulin, Igor B; Baudry, Jerome

    2013-01-01

    Homology models of the E. coli and T. maritima chemotaxis protein CheW were constructed to assess the quality of structural predictions and their applicability in chemotaxis research: i) a model of E. coli CheW was constructed using the T. maritima CheW NMR structure as a template, and ii) a model of T. maritima CheW was constructed using the E. coli CheW NMR structure as a template. The conformational space accessible to the homology models and to the NMR structures was investigated using molecular dynamics and Monte Carlo simulations. The results show that even though static homology models of CheW may be partially structurally different from their corresponding experimentally determined structures, the conformational space they can access through their dynamic variations can be similar, for specific regions of the protein, to that of the experimental NMR structures. When CheW homology models are allowed to explore their local accessible conformational space, modeling can provide a rational path to predicting CheW interactions with the MCP and CheA proteins of the chemotaxis complex. Homology models of CheW (and potentially, of other chemotaxis proteins) should be seen as snapshots of an otherwise larger ensemble of accessible conformational space.

  10. Structural modeling of G-protein coupled receptors: An overview on automatic web-servers.

    Science.gov (United States)

    Busato, Mirko; Giorgetti, Alejandro

    2016-08-01

    Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well.

  11. TJ-II data retrieving by means of a client/server model

    Science.gov (United States)

    Vega, J.; Sánchez, E.; Crémy, C.; Portas, A.; Dulya, C. M.; Nilsson, J.

    1999-01-01

    The database of the TJ-II flexible heliac is centralized in a Unix server. This computer also commands the on-line processes related to data acquisition during TJ-II discharges: programming of measurement systems, connectivity with control systems, data visualization, and computations. The server has to provide access to the data so that signal analysis can be performed by local users or even from remote hosts. Data retrieving is accomplished by means of a client/server architecture in which two data servers are permanently running in the background of the Unix computer. One of them serves data requests from local clients and the other one sends data to remote clients. The communication protocol in both cases has been developed by using TCP/IP and Berkeley sockets. The client part consists of a set of routines (FORTRAN and C callable), which, in a transparent way, provide connectivity with the servers. This structure allows access to TJ-II data exactly in the same way from any computer, hiding not only specific aspects of the database, but hardware architecture of the server computer as well. In addition, the remote access makes it possible to distribute computations and to reduce the load on the Unix server from analysis and visualization tasks. At present, this software is running in four different environments: the Unix server itself, various types of Unix workstations, a CRAY J90 and a CRAY T3E. Finally, due to the fact that visualization is essential for TJ-II data analysis, a powerful and a very flexible visualization tool has been developed. It is a point and click application based on X Window/Motif. Data access is carried out through the client/server processes mentioned above and the software runs in the client computer.

  12. Drug-target interaction prediction: databases, web servers and computational models.

    Science.gov (United States)

    Chen, Xing; Yan, Chenggang Clarence; Zhang, Xiaotian; Zhang, Xu; Dai, Feng; Yin, Jian; Zhang, Yongdong

    2016-07-01

    Identification of drug-target interactions is an important process in drug discovery. Although high-throughput screening and other biological assays are becoming available, experimental methods for drug-target interaction identification remain to be extremely costly, time-consuming and challenging even nowadays. Therefore, various computational models have been developed to predict potential drug-target associations on a large scale. In this review, databases and web servers involved in drug-target identification and drug discovery are summarized. In addition, we mainly introduced some state-of-the-art computational models for drug-target interactions prediction, including network-based method, machine learning-based method and so on. Specially, for the machine learning-based method, much attention was paid to supervised and semi-supervised models, which have essential difference in the adoption of negative samples. Although significant improvements for drug-target interaction prediction have been obtained by many effective computational models, both network-based and machine learning-based methods have their disadvantages, respectively. Furthermore, we discuss the future directions of the network-based drug discovery and network approach for personalized drug discovery based on personalized medicine, genome sequencing, tumor clone-based network and cancer hallmark-based network. Finally, we discussed the new evaluation validation framework and the formulation of drug-target interactions prediction problem by more realistic regression formulation based on quantitative bioactivity data.

  13. Many-server queues with customer abandonment: numerical analysis of their diffusion models

    CERN Document Server

    Dai, J G

    2011-01-01

    We use multidimensional diffusion processes to approximate the dynamics of a queue served by many parallel servers. The queue is served in the first-in-first-out (FIFO) order and the customers waiting in queue may abandon the system without service. Two diffusion models are proposed in this paper. They differ in how the patience time distribution is built into them. The first diffusion model uses the patience time density at zero and the second one uses the entire patience time distribution. To analyze these diffusion models, we develop a numerical algorithm for computing the stationary distribution of such a diffusion process. A crucial part of the algorithm is to choose an appropriate reference density. Using a conjecture on the tail behavior of a limit queue length process, we propose a systematic approach to constructing a reference density. With the proposed reference density, the algorithm is shown to converge quickly in numerical experiments. These experiments also show that the diffusion models are go...

  14. Structure guided homology model based design and engineering of mouse antibodies for humanization.

    Science.gov (United States)

    Kurella, Vinodh B; Gali, Reddy

    2014-01-01

    No universal strategy exists for humanizing mouse antibodies, and most approaches are based on primary sequence alignment and grafting. Although this strategy theoretically decreases the immunogenicity of mouse antibodies, it neither addresses conformational changes nor steric clashes that arise due to grafting of human germline frameworks to accommodate mouse CDR regions. To address these issues, we created and tested a structure-based biologic design approach using a de novo homology model to aid in the humanization of 17 unique mouse antibodies. Our approach included building a structure-based de novo homology model from the primary mouse antibody sequence, mutation of the mouse framework residues to the closest human germline sequence and energy minimization by simulated annealing on the humanized homology model. Certain residues displayed force field errors and revealed steric clashes upon closer examination. Therefore, further mutations were introduced to rationally correct these errors. In conclusion, use of de novo antibody homology modeling together with simulated annealing improved the ability to predict conformational and steric clashes that may arise due to conversion of a mouse antibody into the humanized form and would prevent its neutralization when administered in vivo. This design provides a robust path towards the development of a universal strategy for humanization of mouse antibodies using computationally derived antibody homologous structures.

  15. MetaMQAP: A meta-server for the quality assessment of protein models

    Directory of Open Access Journals (Sweden)

    Bujnicki Janusz M

    2008-09-01

    _TS scores. Local model accuracy predicted by MetaMQAP shows an impressive correlation coefficient of 0.7 with true deviations from native structures, a significant improvement over all constituent primary MQAP scores. The global MetaMQAP score is correlated with model GDT_TS on the level of 0.89. Conclusion Finally, we compared our method with the MQAPs that scored best in the 7th edition of CASP, using CASP7 server models (not included in the MetaMQAP training set as the test data. In our benchmark, MetaMQAP is outperformed only by PCONS6 and method QA_556 – methods that require comparison of multiple alternative models and score each of them depending on its similarity to other models. MetaMQAP is however the best among methods capable of evaluating just single models. We implemented the MetaMQAP as a web server available for free use by all academic users at the URL https://genesilico.pl/toolkit/

  16. Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling

    Directory of Open Access Journals (Sweden)

    Harrison Ndung'u Mwangi

    2017-01-01

    Full Text Available Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS–MODEL were used to generate the 40S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation (RMSD value of 3.9 Å relative to the template׳s crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying this approach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.

  17. Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling.

    Science.gov (United States)

    Mwangi, Harrison Ndung'u; Wagacha, Peter; Mathenge, Peterson; Sijenyi, Fredrick; Mulaa, Francis

    2017-01-01

    Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS-MODEL were used to generate the 40S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation (RMSD) value of 3.9 Å relative to the template׳s crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying this approach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.

  18. Homology modeling of the serotonin transporter: Insights into the primary escitalopram-binding Site

    DEFF Research Database (Denmark)

    Jørgensen, Anne Marie; Tagmose, L.; Jørgensen, A.M.M.

    2007-01-01

    -ray structure of the closely related amino acid transporter, Aquifex aeolicus leucine transporter (LeuT), provides an opportunity to develop a three-dimensional model of the structure of SERT. We present herein a homology model of SERT using LeuT as the template and containing escitalopram as a bound ligand...

  19. Homology Modelling of the GABA Transporter and Analysis of Tiagabine Binding

    DEFF Research Database (Denmark)

    Skovstrup, S.; Taboureau, Olivier; Bräuner-Osborne, H.

    2010-01-01

    A homology model of the human GABA transporter (GAT-1) based on the recently reported crystal structures of the bacterial leucine transporter from Aquifex aeolicus (LeuT) was developed. The stability of the resulting model embedded in a membrane environment was analyzed by extensive molecular...

  20. Impact of template choice on homology model efficiency in virtual screening.

    Science.gov (United States)

    Rataj, Krzysztof; Witek, Jagna; Mordalski, Stefan; Kosciolek, Tomasz; Bojarski, Andrzej J

    2014-06-23

    Homology modeling is a reliable method of predicting the three-dimensional structures of proteins that lack NMR or X-ray crystallographic data. It employs the assumption that a structural resemblance exists between closely related proteins. Despite the availability of many crystal structures of possible templates, only the closest ones are chosen for homology modeling purposes. To validate the aforementioned approach, we performed homology modeling of four serotonin receptors (5-HT1AR, 5-HT2AR, 5-HT6R, 5-HT7R) for virtual screening purposes, using 10 available G-Protein Coupled Receptors (GPCR) templates with diverse evolutionary distances to the targets, with various approaches to alignment construction and model building. The resulting models were further validated in two steps by means of ligand docking and enrichment calculation, using Glide software. The final quality of the models was determined in virtual screening-like experiments by the AUROC score of the resulting ROC curves. The outcome of this research showed that no correlation between sequence identity and model quality was found, leading to the conclusion that the closest phylogenetic relative is not always the best template for homology modeling.

  1. Gclust Server: 137081 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 137081 SCE_YOL159C-A Cluster Sequences - 90 hypothetical protein identified by homology. See FEBS Letters...ngth 90 Representative annotation hypothetical protein identified by homology. See FEBS Letters

  2. Gclust Server: 158645 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 158645 SCE_YML007C-A Cluster Sequences - 36 hypothetical protein identified by homology. See FEBS Letters...ngth 36 Representative annotation hypothetical protein identified by homology. See FEBS Letters

  3. Gclust Server: 174923 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 174923 SCE_YMR013W-A Cluster Sequences - 26 hypothetical protein identified by homology. See FEBS Letters...ngth 26 Representative annotation hypothetical protein identified by homology. See FEBS Letters

  4. Gclust Server: 184262 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 184262 SCE_YDL159W-A Cluster Sequences - 43 hypothetical protein identified by homology. See FEBS Letters...ngth 43 Representative annotation hypothetical protein identified by homology. See FEBS Letters

  5. Gclust Server: 79042 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available Arabidopsis ABC transporter homolog 12); ATPase, coupled to transmembrane movement of substances 1 1.00e-40 ...transmembrane movement of substances Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-40 Plants a

  6. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    Science.gov (United States)

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  7. Comparative homology modeling of human rhodopsin with several ...

    African Journals Online (AJOL)

    Yomi

    2012-01-05

    Jan 5, 2012 ... humble effort has been made to identify and remove the loopholes in the existing structure (1EDS) and model the 3D structure ... as seen in the cryo-electron microscopy studies, with the ... cannot be obtained or dissolved in large enough ... of non-bonded interaction between different atom types was done.

  8. Three-Dimensional Structure of Arabidopsis thaliana Lipase Predicted by Homology Modeling Method

    OpenAIRE

    2011-01-01

    Triacylglycerol lipases have been thoroughly characterized in mammals and microorganisms. By contrast, very little is known about plant lipases. In this investigation, a homology model of Arabidopsis thaliana lipase (NP_179126) was constructed using a human gastric lipase (PDB ID: 1HLG), as a template for model building. This model was then assessed for stereochemical quality and side chain environment. Natural substrates: tributyrin, trioctanoin and triolen were docked into the model to inve...

  9. Learning SQL Server Reporting Services 2012

    CERN Document Server

    Krishnaswamy, Jayaram

    2013-01-01

    The book is packed with clear instructions and plenty of screenshots, providing all the support and guidance you will need as you begin to generate reports with SQL Server 2012 Reporting Services.This book is for those who are new to SQL Server Reporting Services 2012 and aspiring to create and deploy cutting edge reports. This book is for report developers, report authors, ad-hoc report authors and model developers, and Report Server and SharePoint Server Integrated Report Server administrators. Minimal knowledge of SQL Server is assumed and SharePoint experience would be helpful.

  10. Illustrating and homology modeling the proteins of the Zika virus [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2016-09-01

    Full Text Available The Zika virus (ZIKV is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

  11. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

    Science.gov (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.

  12. [Preparation of monoclonal antibody against 4-amylphenol and homology modeling of its Fv fragment].

    Science.gov (United States)

    Cheng, Lei; Wu, Haizhen; Fei, Jing; Zhang, Lujia; Ye, Jiang; Zhang, Huizhan

    2017-03-01

    Objective To prepare and characterize a monoclonal antibody (mAb) against 4-amylphenol (4-AP), clone its cDNA sequence and make homology modeling for its Fv fragment. Methods A high-affinity anti-4-AP mAb was generated from a hybridoma cell line F10 using electrofusion between splenocytes from APA-BSA-immunized mouse and Sp2/0 myeloma cells. Then we extracted the mRNA of F10 cells and cloned the cDNA of mAb. The homology modeling and molecular docking of its Fv fragment was conducted with biological software. Results Under the optimum conditions, the ic-ELISA equation was y=A2+(A1-A2)/(1+(x/x0)(p)) (A1=1.28; A2=-0.066; x0=12560.75; p=0.74) with a correlation coefficient (R(2)) of 0.997. The lowest detectable limit was 0.65 μg/mL. The heavy and light chains of mAb respectively belonged to IgG1 and Kappa. The homology modeling and molecular docking studies revealed that the binding of 4-Ap and mAb was attributed to the hydrogen bond and hydrophobic interactions. Conclusion The study successfully established a stable 4-AP mAb-secreting hybridoma cell line. The study on spatial structure of Fv fragment using homology modeling provided a reference for the development and design of single chain variable fragments.

  13. Homology modeling of the three membrane proteins of the dhurrin metabolon

    DEFF Research Database (Denmark)

    Jensen, Kenneth; Osmani, Sarah Anne; Hamann, Thomas

    2011-01-01

    is derived from l-tyrosine in a pathway involving the two cytochromes P450 (CYPs) CYP79A1 and CYP71E1, a glucosyltransferase (UGT85B1), and the redox partner NADPH-dependent cytochrome P450 reductase (CPR). Experimental evidence suggests that the enzymes of this pathway form a metabolon. Homology modeling...

  14. A homology model of Xyloglucan Xylosyltransferase 2 reveals critical amino acids involved in substrate binding.

    Science.gov (United States)

    Culbertson, Alan T; Tietze, Alesia A; Tietze, Daniel; Chou, Yi-Hsiang; Smith, Adrienne L; Young, Zachary T; Zabotina, Olga A

    2016-09-01

    In dicotyledonous plants, xyloglucan (XyG) is the most abundant hemicellulose of the primary cell wall. The enzymes involved in XyG biosynthesis have been identified through reverse-genetics and activity was characterized by heterologous expression. Currently, there is no information on the atomic structures or amino acids involved in activity or substrate binding of any of the Golgi-localized XyG biosynthetic enzymes. A homology model of the xyloglucan xylosyltransferase 2 (XXT2) catalytic domain was built on the basis of the crystal structure of A64Rp. Molecular dynamics simulations revealed that the homology model retains the glycosyltransferase (GT)-A fold of the template structure used to build the homology model indicating that XXT2 likely has a GT-A fold. According to the XXT2 homology model, six amino acids (Phe204, Lys207, Asp228, Ser229, Asp230, His378) were selected and their contribution in catalytic activity was investigated. Site-directed mutagenesis studies show that Asp228, Asp230 and His378 are critical for XXT2 activity and are predicted to be involved in coordination of manganese ion. Lys207 was also found to be critical for protein activity and the homology model indicates a critical role in substrate binding. Additionally, Phe204 mutants have less of an impact on XXT2 activity with the largest effect when replaced with a polar residue. This is the first study that investigates the amino acids involved in substrate binding of the XyG-synthesizing xylosyltransferases and contributes to the understanding of the mechanisms of polysaccharide-synthesizing GTs and XyG biosynthesis. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. PDBalert: automatic, recurrent remote homology tracking and protein structure prediction

    Directory of Open Access Journals (Sweden)

    Söding Johannes

    2008-11-01

    Full Text Available Abstract Background During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template. When no homologs can be found in the protein structure database (PDB, the user would need to rerun the same search at regular intervals in order to make timely use of a template once it becomes available. Results PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the sequences on hold. The mail contains links to the search results and to an automatically generated 3D homology model. The sequence search is performed with the same software as used by the very sensitive and reliable remote homology detection server HHpred, which is based on pairwise comparison of Hidden Markov models. Conclusion PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest.

  16. Parallel Computing Using Web Servers and "Servlets".

    Science.gov (United States)

    Lo, Alfred; Bloor, Chris; Choi, Y. K.

    2000-01-01

    Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

  17. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction

    Science.gov (United States)

    Zhu, Kai; Day, Tyler; Warshaviak, Dora; Murrett, Colleen; Friesner, Richard; Pearlman, David

    2017-01-01

    We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA-II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics-based energy function (VSGB2.0), which improves the model quality significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived antibodies in this assessment, the average RMSDs for the homology model Fv and framework regions are 1.19 Å and 0.74 Å, respectively. The average RMSDs for five non-H3 CDR loops range from 0.61 Å to 1.05 Å, and the H3 loop average RMSD is 2.91 Å using our knowledge-based loop prediction approach. The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure. Notably, our method for predicting the H3 loop in the crystal structure environment ranked first among the seven participating groups in AMA-II, and our method made the best prediction among all participants for seven of the ten targets. PMID:24619874

  18. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction.

    Science.gov (United States)

    Zhu, Kai; Day, Tyler; Warshaviak, Dora; Murrett, Colleen; Friesner, Richard; Pearlman, David

    2014-08-01

    We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA-II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics-based energy function (VSGB2.0), which improves the model quality significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived antibodies in this assessment, the average RMSDs for the homology model Fv and framework regions are 1.19 Å and 0.74 Å, respectively. The average RMSDs for five non-H3 CDR loops range from 0.61 Å to 1.05 Å, and the H3 loop average RMSD is 2.91 Å using our knowledge-based loop prediction approach. The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure. Notably, our method for predicting the H3 loop in the crystal structure environment ranked first among the seven participating groups in AMA-II, and our method made the best prediction among all participants for seven of the ten targets. © 2014 Wiley Periodicals, Inc.

  19. Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism

    Science.gov (United States)

    Ramachandran, Srinivas; Dokholyan, Nikolay V.

    Geneticists and molecular and cell biologists routinely uncover new proteins important in specific biological processes/pathways. However, either the molecular functions or the functional mechanisms of many of these proteins are unclear due to a lack of knowledge of their atomic structures. Yet, determining experimental structures of many proteins presents technical challenges. The current methods for obtaining atomic-resolution structures of biomolecules (X-ray crystallography and NMR spectroscopy) require pure preparations of proteins at concentrations much higher than those at which the proteins exist in a physiological environment. Additionally, NMR has size limitations, with current technology limited to the determination of structures of proteins with masses of up to 15 kDa. Due to these reasons, atomic structures of many medically and biologically important proteins do not exist. However, the structures of these proteins are essential for several purposes, including in silico drug design [1], understanding the effects of disease mutations [2], and designing experiments to probe the functional mechanisms of proteins. Comparative modeling has gained importance as a tool for bridging the gap between sequence and structure space, allowing researchers to build structural models of proteins that are difficult to crystallize or for which structure determination by NMR spectroscopy is not tractable. Comparative modeling, or homology modeling, exploits the fact that two proteins whose sequences are evolutionarily connected display similar structural features [3]. Thus, the known structure of a protein (template) can be used to generate a molecular model of the protein (query) whose experimental structure is notknown.

  20. Modeling of high homologous temperature deformation behavior for stress and life-time analyses

    Energy Technology Data Exchange (ETDEWEB)

    Krempl, E. [Rensselaer Polytechnic Institute, Troy, NY (United States)

    1997-12-31

    Stress and lifetime analyses need realistic and accurate constitutive models for the inelastic deformation behavior of engineering alloys at low and high temperatures. Conventional creep and plasticity models have fundamental difficulties in reproducing high homologous temperature behavior. To improve the modeling capabilities {open_quotes}unified{close_quotes} state variable theories were conceived. They consider all inelastic deformation rate-dependent and do not have separate repositories for creep and plasticity. The viscoplasticity theory based on overstress (VBO), one of the unified theories, is introduced and its properties are delineated. At high homologous temperature where secondary and tertiary creep are observed modeling is primarily accomplished by a static recovery term and a softening isotropic stress. At low temperatures creep is merely a manifestation of rate dependence. The primary creep modeled at low homologous temperature is due to the rate dependence of the flow law. The model is unaltered in the transition from low to high temperature except that the softening of the isotropic stress and the influence of the static recovery term increase with an increase of the temperature.

  1. Gclust Server: 9987 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available DOPSIS HOMOLOG OF YEAST ERGOSTEROL28) 11 1.00e-40 57.14 11.11 0.0 0.0 0.0 62.5 Show 9987 Cluster ID 9987 Seq...d Sequences(2) Sequence length 129 Representative annotation ERG28 (ARABIDOPSIS HOMOLOG OF YEAST ERGOSTERO

  2. Gclust Server: 1356 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available the large ribosomal subunit, has homologs in plants and animals 60 1.00e-70 71.43 55.56 100.0 0.0 22.58 100....nctions in assembly of the large ribosomal subunit, has homologs in plants and animals

  3. Gclust Server: 22367 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available f two yeast homologs (with Sdo1p/Ylr022cp) of the human protein SBDS responsible for autosomal recessive Shwachman-Bodian-Diamond...m, one of two yeast homologs (with Sdo1p/Ylr022cp) of the human protein SBDS responsible for autosomal recessive Shwachman-Bodian-Dia...mond Syndrome, also conserved in Archaea Number of Seque

  4. Gclust Server: 7628 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available CTED: similar to PMS1 protein homolog 2 (DNA mismatch repair protein PMS2) ; no annotation 14 1.00e-45 0.0 0...sentative annotation XP_001126131.1 PREDICTED: similar to PMS1 protein homolog 2 (DNA mismatch repair protein PMS2

  5. Gclust Server: 46843 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 46843 CEL_Y54F10AL.2_17556156 Cluster Sequences Related Sequences(23) 461 est-1: EST (Ever Shorter Telomeres...t-1: EST (Ever Shorter Telomeres) homolog family member (est-1) Number of Sequences 2 Homologs 2 Clustering ... sequences Related Sequences(23) Sequence length 461 Representative annotation es

  6. Gclust Server: 73565 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available BC2 homolog 4); ATPase, coupled to transmembrane movement of substances 1 1.00e-40 14.29 0.0 0.0 0.0 0.0 0.0...ve annotation ATATH4 (ABC2 homolog 4); ATPase, coupled to transmembrane movement of substances Number of Seq

  7. Gclust Server: 73859 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available BC2 homolog 2); ATPase, coupled to transmembrane movement of substances 1 1.00e-31 14.29 0.0 0.0 0.0 0.0 0.0...ve annotation ATATH2 (ABC2 homolog 2); ATPase, coupled to transmembrane movement of substances Number of Seq

  8. Gclust Server: 73561 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available BC2 homolog 6); ATPase, coupled to transmembrane movement of substances 1 9.98e-01 14.29 0.0 0.0 0.0 0.0 0.0...ve annotation ATATH6 (ABC2 homolog 6); ATPase, coupled to transmembrane movement of substances Number of Seq

  9. Gclust Server: 73000 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available BC2 homolog 7); ATPase, coupled to transmembrane movement of substances 1 9.98e-01 14.29 0.0 0.0 0.0 0.0 0.0...ve annotation ATATH7 (ABC2 homolog 7); ATPase, coupled to transmembrane movement of substances Number of Seq

  10. Gclust Server: 73566 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ABC2 homolog 16); ATPase, coupled to transmembrane movement of substances 1 1.00e-40 14.29 0.0 0.0 0.0 0.0 0...tive annotation ATATH16 (ABC2 homolog 16); ATPase, coupled to transmembrane movement of substances Number of

  11. Gclust Server: 73987 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available BC2 homolog 3); ATPase, coupled to transmembrane movement of substances 1 1.00e-35 14.29 0.0 0.0 0.0 0.0 0.0...ve annotation ATATH3 (ABC2 homolog 3); ATPase, coupled to transmembrane movement of substances Number of Seq

  12. Gclust Server: 73972 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ABC2 homolog 14); ATPase, coupled to transmembrane movement of substances 1 1.00e-35 14.29 0.0 0.0 0.0 0.0 0...tive annotation ATATH14 (ABC2 homolog 14); ATPase, coupled to transmembrane movement of substances Number of

  13. Gclust Server: 74752 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available BC2 homolog 5); ATPase, coupled to transmembrane movement of substances 1 1.00e-31 14.29 0.0 0.0 0.0 0.0 0.0...ve annotation ATATH5 (ABC2 homolog 5); ATPase, coupled to transmembrane movement of substances Number of Seq

  14. Gclust Server: 77039 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ABC2 homolog 15); ATPase, coupled to transmembrane movement of substances 1 1.00e-35 14.29 0.0 0.0 0.0 0.0 0...tive annotation ATATH15 (ABC2 homolog 15); ATPase, coupled to transmembrane movement of substances Number of

  15. Gclust Server: 77003 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 77003 ATH_AT5G54650_15239699 Cluster Sequences - 900 Fh5 (FORMIN HOMOLOGY5); actin ...OLOGY5); actin binding Number of Sequences 1 Homologs 1 ...Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 900 Representative annotation Fh5 (FORMIN HOM

  16. Gclust Server: 76964 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 76964 ATH_AT5G54650_30696498 Cluster Sequences - 900 Fh5 (FORMIN HOMOLOGY5); actin ...OLOGY5); actin binding Number of Sequences 1 Homologs 1 ...Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 900 Representative annotation Fh5 (FORMIN HOM

  17. SLC4A11 Three-Dimensional Homology Model Rationalizes Corneal Dystrophy-Causing Mutations.

    Science.gov (United States)

    Badior, Katherine E; Alka, Kumari; Casey, Joseph R

    2017-03-01

    We studied the structural effects of point mutations of a membrane protein that cause genetic disease. SLC4A11 is a membrane transport protein (OH(-) /H(+) /NH3 /H2 O) of basolateral corneal endothelium, whose mutations cause some cases of congenital hereditary endothelial dystrophy and Fuchs endothelial corneal dystrophy. We created a three-dimensional homology model of SLC4A11 membrane domain, using Band 3 (SLC4A1) crystal structure as template. The homology model was assessed in silico and by analysis of mutants designed on the basis of the model. Catalytic pathway mutants p.Glu675Gln, p.His724Arg, and p.His724Ala impaired SLC4A11 transport. p.Ala720Leu, in a region of extended structure of the proposed translocation pore, failed to mature to the cell surface. p.Gly509Lys, located in an open region at the core domain/gate domain interface, had wild-type level of transport function. The molecular phenotype of 37 corneal dystrophy-causing point mutants was rationalized, based on their location in the homology model. Four map to the substrate translocation pathway, 25 to regions of close transmembrane helix packing, three to the dimeric interface, and five lie in extramembraneous loops. The model provides a view of the spectrum of effects of disease mutations on membrane protein structure and provides a tool to analyze pathogenicity of additional newly discovered SLC4A11 mutants. © 2016 WILEY PERIODICALS, INC.

  18. CPU Server

    CERN Multimedia

    The CERN computer centre has hundreds of racks like these. They are over a million times more powerful than our first computer in the 1960's. This tray is a 'dual-core' server. This means it effectively has two CPUs in it (eg. two of your home computers minimised to fit into a single box). Also note the copper cooling fins, to help dissipate the heat.

  19. Ligand-guided homology modelling of the GABAB2 subunit of the GABAB receptor.

    Science.gov (United States)

    Freyd, Thibaud; Warszycki, Dawid; Mordalski, Stefan; Bojarski, Andrzej J; Sylte, Ingebrigt; Gabrielsen, Mari

    2017-01-01

    γ-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system, and disturbances in the GABAergic system have been implicated in numerous neurological and neuropsychiatric diseases. The GABAB receptor is a heterodimeric class C G protein-coupled receptor (GPCR) consisting of GABAB1a/b and GABAB2 subunits. Two GABAB receptor ligand binding sites have been described, namely the orthosteric GABA binding site located in the extracellular GABAB1 Venus fly trap domain and the allosteric binding site found in the GABAB2 transmembrane domain. To date, the only experimentally solved three-dimensional structures of the GABAB receptor are of the Venus fly trap domain. GABAB receptor allosteric modulators, however, show great therapeutic potential, and elucidating the structure of the GABAB2 transmembrane domain may lead to development of novel drugs and increased understanding of the allosteric mechanism of action. Despite the lack of x-ray crystal structures of the GABAB2 transmembrane domain, multiple crystal structures belonging to other classes of GPCRs than class A have been released within the last years. More closely related template structures are now available for homology modelling of the GABAB receptor. Here, multiple homology models of the GABAB2 subunit of the GABAB receptor have been constructed using templates from class A, B and C GPCRs, and docking of five clusters of positive allosteric modulators and decoys has been undertaken to select models that enrich the active compounds. Using this ligand-guided approach, eight GABAB2 homology models have been chosen as possible structural representatives of the transmembrane domain of the GABAB2 subunit. To the best of our knowledge, the present study is the first to describe homology modelling of the transmembrane domain of the GABAB2 subunit and the docking of positive allosteric modulators in the receptor.

  20. A benchmark testing ground for integrating homology modeling and protein docking.

    Science.gov (United States)

    Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J; Bonvin, Alexandre M J J; Weng, Zhiping; Vajda, Sandor; Schueler-Furman, Ora; Kozakov, Dima

    2017-01-01

    Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in

  1. Gclust Server: 40285 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 40285 CEL_K11D12.10_25149258 Cluster Sequences Related Sequences(288) 978 mlk-1: human MLK...ted sequences Related Sequences(288) Sequence length 978 Representative annotation mlk-1: human MLK... (Mixed Lineage Kinase) homolog family member (mlk-1) 2 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 40285 ... (Mixed Lineage Kinase) homolog family member (mlk-1) Number of Sequences 2 Homologs 2 Clu

  2. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    Science.gov (United States)

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  3. Gclust Server: 111909 [Gclust Server

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    Full Text Available ing, interacts with the branchpoint-binding protein during the formation of the second commitment complex 1 ... during the formation of the second commitment complex Number of Sequences 1 Homologs 1 Clustering threshold

  4. Gclust Server: 182697 [Gclust Server

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    Full Text Available mber of Sequences 1 Homologs 1 Clustering threshold 1.00e-50 Plants and algae (7s...pecies) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 0.

  5. Gclust Server: 61662 [Gclust Server

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    Full Text Available species) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 0...umber of Sequences 2 Homologs 2 Clustering threshold 1.00e-40 Plants and algae (7

  6. Gclust Server: 178261 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available mber of Sequences 1 Homologs 1 Clustering threshold 1.00e-35 Plants and algae (7s...pecies) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 0.

  7. Gclust Server: 156492 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available species) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 4...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-16 Plants and algae (7

  8. Gclust Server: 168978 [Gclust Server

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    Full Text Available species) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 4...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-35 Plants and algae (7

  9. Gclust Server: 185474 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available species) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 4...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-25 Plants and algae (7

  10. Gclust Server: 99490 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available species) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 0...RIPTION REGULATOR PROTEIN Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-08 Plants and algae (7

  11. Gclust Server: 150355 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available eshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalveolata, ...tation hypothetical protein chr_0_8254752_8; no annotation Number of Sequences 1 Homologs 1 Clustering thr

  12. Gclust Server: 117008 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 328 Representative annotation components of type IV pilus Number of Sequences 1 Homologs 1 Clustering thre...shold 1.00e-70 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalveolata, E

  13. Gclust Server: 3369 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available Homologs 29 Clustering threshold 1.00e-60 Plants and algae (7species) (%) 71.43 Other Bikonts (Chromalveolat...ngth 493 Representative annotation CER1 protein, putative Number of Sequences 29

  14. Gclust Server: 114867 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available eshold 1.00e-80 Plants and algae (7species) (%) 14.29 Other Bikonts (Chromalveolata...Representative annotation fgenesh4_pg.C_scaffold_787000001 Number of Sequences 1 Homologs 1 Clustering thr

  15. Gclust Server: 142884 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 1 Homologs 1 Clustering threshold 1.00e-08 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalveolata...otation hypothetical protein chr_0_8254435_96; no annotation Number of Sequences

  16. Gclust Server: 29839 [Gclust Server

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    Full Text Available ponse regulator, part of a two-component signal transducer that mediates osmosensing via a phosphorelay mech...nal transducer that mediates osmosensing via a phosphorelay mechanism Number of Sequences 3 Homologs 3 Clust

  17. Gclust Server: 83918 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available quence length 343 Representative annotation protein kinase family protein Number ...of Sequences 1 Homologs 1 Clustering threshold 1.00e-70 Plants and algae (7species) (%) 14.29 Other Bikonts (Chromalve

  18. Gclust Server: 184554 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 6 Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 88 Representative ...ces 1 Homologs 1 Clustering threshold 1.00e-40 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalveo

  19. Gclust Server: 38415 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available k to related sequences - Sequence length 604 Representative annotation - Number of Sequences 3 Homologs 3 Cl...ustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  20. Gclust Server: 184178 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available to cluster sequences Cluster Sequences Link to related sequences - Sequence length 296 Representative annot... Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalveolata,

  1. Gclust Server: 109146 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available HSA_4505205 Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 476 Representative...annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e+00 Plants and algae (7species) (%) 0.

  2. Gclust Server: 14789 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ce length 231 Representative annotation replication protein-related Number of Seq...uences 7 Homologs 7 Clustering threshold 1.00e-50 Plants and algae (7species) (%) 14.29 Other Bikonts (Chromalve

  3. Gclust Server: 34469 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ate chain, acts in the cytoplasmic dynein pathway, forms cortical cytoplasmic microtubule capture site with ...thway, forms cortical cytoplasmic microtubule capture site with Num1p Number of Sequences 3 Homologs 3 Clust

  4. Gclust Server: 101443 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 101443 CEL_C16C2.3_17505597 Cluster Sequences Related Sequences(153) 753 ocrl-1: OCRL (Lowe's oculocerebro...ntative annotation ocrl-1: OCRL (Lowe's oculocerebrorenal syndrome protein) homolog family member (ocrl-1) N

  5. Gclust Server: 1365 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available YLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT ISOZYME) PROT...LTRANSFERASE (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT ISOZYME) PROTEIN Number of Sequences 59 Homologs 59

  6. Gclust Server: 149031 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available oskeleton and is involved in chromatin organization and nuclear transport, interacts genetically with TCP1 a...ganization and nuclear transport, interacts genetically with TCP1 and ICY1 Number of Sequences 1 Homologs 1

  7. Gclust Server: 18750 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 18750 SCE_YIL156W-B Cluster Sequences - 73 Putative protein of unknown function, original... protein of unknown function, originally identified based on homology to Ashbya gossypii and other related y

  8. Gclust Server: 58216 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 58216 HSA_21237732 Cluster Sequences - 377 NP_631941.1 megalencephalic leukoencephalopathy with subcortical...leukoencephalopathy with subcortical cysts 1 gene product ; no annotation Number of Sequences 2 Homologs 2 C

  9. Gclust Server: 83041 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available old 1.00e-28 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0...nnotation hypothetical protein Number of Sequences 1 Homologs 1 Clustering thresh

  10. Gclust Server: 49169 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available CTED: similar to Zinc finger FYVE domain-containing protein 9 (Mothers against decapentaplegic homolog-inter....1 PREDICTED: similar to Zinc finger FYVE domain-containing protein 9 (Mothers ag

  11. Gclust Server: 7761 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 7761 ATH_AT4G20410_18415496 Cluster Sequences Related Sequences(19) 291 GSNAP (GAMMA-SOLUBLE NSF ATTACHMENT...ion GSNAP (GAMMA-SOLUBLE NSF ATTACHMENT PROTEIN); intracellular transporter Number of Sequences 14 Homologs

  12. Homology modelling and docking analysis of L-lactate dehydrogenase from Streptococcus thermopilus

    Directory of Open Access Journals (Sweden)

    Vukić Vladimir R.

    2016-01-01

    Full Text Available The aim of this research was to create a three-dimensional model of L-lactate dehydrogenase from the main yoghurt starter culture - Streptococcus thermopilus, to analyse its structural features and investigate substrate binding in the active site. NCBI BlastP was used against the Protein Data Bank database in order to identify the template for construction of homology models. Multiple sequence alignment was performed using the program MUSCULE within the UGENE 1.11.3 program. Homology models were constructed using the program Modeller v. 9.17. The obtained 3D model was verified by Ramachandran plots. Molecular docking simulations were performed using the program Surflex-Dock. The highest sequence similarity was observed with L-lactate dehydrogenase from Lactobacillus casei subsp. casei, with 69% identity. Therefore, its structure (PDB ID: 2ZQY:A was selected as a modelling template for homology modelling. Active residues are by sequence similarity predicted: S. thermophilus - HIS181 and S. aureus - HIS179. Binding energy of pyruvate to L-lactate dehydrogenase of S. thermopilus was - 7.874 kcal/mol. Pyruvate in L-lactate dehydrogenase of S. thermopilus makes H bonds with catalytic HIS181 (1.9 Å, as well as with THR235 (3.6 Å. Although our results indicate similar position of substrates between L-lactate dehydrogenase of S. thermopilus and S. aureus, differences in substrate distances and binding energy values could influence the reaction rate. Based on these results, the L-lactate dehydrogenase model proposed here could be used as a guide for further research, such as transition states of the reaction through molecular dynamics. [Projekat Ministarstva nauke Republike Srbije, br. III 46009

  13. Determination and validation of mTOR kinase-domain 3D structure by homology modeling

    Directory of Open Access Journals (Sweden)

    Lakhlili W

    2015-07-01

    Full Text Available Wiame Lakhlili,1 Gwénaël Chevé,2 Abdelaziz Yasri,2 Azeddine Ibrahimi1 1Laboratoire de Biotechnologie (MedBiotech, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V de Rabat, Rabat, Morroco; 2OriBase Pharma, Cap Gamma, Parc Euromédecine, Montpellier, France Abstract: The AKT/mammalian target of rapamycin (mTOR pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.Keywords: mTOR, homology modeling, mTOR kinase-domain, docking

  14. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs.

    Science.gov (United States)

    Bloom, Jesse D

    2014-10-01

    Phylogenetic analyses of molecular data require a quantitative model for how sequences evolve. Traditionally, the details of the site-specific selection that governs sequence evolution are not known a priori, making it challenging to create evolutionary models that adequately capture the heterogeneity of selection at different sites. However, recent advances in high-throughput experiments have made it possible to quantify the effects of all single mutations on gene function. I have previously shown that such high-throughput experiments can be combined with knowledge of underlying mutation rates to create a parameter-free evolutionary model that describes the phylogeny of influenza nucleoprotein far better than commonly used existing models. Here, I extend this work by showing that published experimental data on TEM-1 beta-lactamase (Firnberg E, Labonte JW, Gray JJ, Ostermeier M. 2014. A comprehensive, high-resolution map of a gene's fitness landscape. Mol Biol Evol. 31:1581-1592) can be combined with a few mutation rate parameters to create an evolutionary model that describes beta-lactamase phylogenies much better than most common existing models. This experimentally informed evolutionary model is superior even for homologs that are substantially diverged (about 35% divergence at the protein level) from the TEM-1 parent that was the subject of the experimental study. These results suggest that experimental measurements can inform phylogenetic evolutionary models that are applicable to homologs that span a substantial range of sequence divergence.

  15. Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.

    Science.gov (United States)

    Blaszczyk, Maciej; Kurcinski, Mateusz; Kouza, Maksim; Wieteska, Lukasz; Debinski, Aleksander; Kolinski, Andrzej; Kmiecik, Sebastian

    2016-01-15

    Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  16. DockoMatic 2.0: high throughput inverse virtual screening and homology modeling.

    Science.gov (United States)

    Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T; McDougal, Owen M; Andersen, Timothy L

    2013-08-26

    DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly graphical user interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to (1) conduct high throughput inverse virtual screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELER programs and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education.

  17. DockoMatic 2.0: High Throughput Inverse Virtual Screening and Homology Modeling

    Science.gov (United States)

    Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T.; McDougal, Owen M.; Andersen, Timothy L.

    2013-01-01

    DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly Graphical User Interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to: (1) conduct high throughput Inverse Virtual Screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying a receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories, and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELLER programs, and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education. PMID:23808933

  18. n Silico Analysis of Envelope Dengue Virus-2 and Envelope Dengue Virus-3 Protein as the Backbone of Dengue Virus Tetravalent Vaccine by Using Homology Modeling Method

    Directory of Open Access Journals (Sweden)

    Rizky I. Taufik

    2009-01-01

    Full Text Available Problem statement: Dengue fever, which was caused by Dengue virus infection, had became a major public health problem in the tropic and subtropical countries. Dengue virus (DENV had four serotypes (DENV-1, DENV-2, DENV-3 and DENV-4, based on their immunogenic in the human body. Preventive measure will be necessary to decrease the prevalence of dengue fever, by developing modern vaccine. Approach: This research was focused on in silico study of dengue virus vaccines, by using envelope (E protein of DENV-2 and DENV-3 as their backbones. T cell epitope prediction was determined by using MULTIPRED server and B cell epitope prediction was determined by using Conformational Epitope Prediction server (CEP. Homology modeling study of E DENV-3 protein as the vaccine backbone had produced six dengue vaccine peptides (HMM Vaccine 1-6. Moreover, homology modeling study of E DENV-2 protein as vaccine backbone had produced six dengue vaccine peptides (ANN vaccine 1-6. Results: The BLAST analysis of HMM and ANN vaccines had produced 93% and 91% identity, respectively. The Ramachandran Plot of both vaccines had shown less than 15% non glycine residue in the disallowed region, therefore it showed the solid stability of the proteins. The VAST analysis of E DENV-3 backbone vaccines had determined, that HMM4 and HMM6 had the highest structure similarity with native E DENV-3. HMM4 and HMM6 had the highest VAST score of 64.5. Moreover, the VAST analysis of E DENV-2 backbone vaccines had determined, that ANN1, ANN3, ANN4, ANN5 and ANN6 had the highest structure similarity with native E DENV-2. ANN1, ANN3, ANN4, ANN5 and ANN6 have the highest VAST score of 64.7. Conclusion/Recommendation: It could be inferred from this research that HMM4; HMM6; ANN1; ANN3; ANN4; ANN5; and ANN6 were the best in silico vaccine design, based on their similarity with native E DENV Proteins. This research could be applied for the wet

  19. Space constrained homology modelling: the paradigm of the RNA-dependent RNA polymerase of dengue (type II) virus.

    Science.gov (United States)

    Vlachakis, Dimitrios; Kontopoulos, Dimitrios Georgios; Kossida, Sophia

    2013-01-01

    Protein structure is more conserved than sequence in nature. In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape. Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus. The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp. The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure. The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling. Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures.

  20. Gclust Server: 16861 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 16861 CEL_C34G6.6_25144184 Cluster Sequences Related Sequences(21) 1069 noah-1: NOm...pA Homolog (Drosophila nompA: no mechanoreceptor potential A) family member (noah-1) 6 1.00e-50 0.0 0.0 0.0 ...presentative annotation noah-1: NOmpA Homolog (Drosophila nompA: no mechanoreceptor potential A) family member (noah...Sequences Link to related sequences Related Sequences(21) Sequence length 1069 Re

  1. A novel measurement method for the morphology of the mandibular ramus using homologous modelling.

    Science.gov (United States)

    Inoue, K; Nakano, H; Sumida, T; Yamada, T; Otawa, N; Fukuda, N; Nakajima, Y; Kumamaru, W; Mishima, K; Kouchi, M; Takahashi, I; Mori, Y

    2015-01-01

    It is important to assess the mandibular morphology when orthognathic surgery, especially mandibular ramus osteotomy, is performed. Several studies on three-dimensional (3D) facial asymmetry have reported differences in linear and angle measurements between the deviated and contralateral sides in asymmetric mandibles. However, methods used in these studies cannot analyse the 3D morphology of the ramus. In this study, we aimed to evaluate the differences in mandibular ramus between the deviated and contralateral sides in asymmetric mandibles using traditional measurements as well as 3D shape analysis. 15 Japanese females with jaw deformities treated by orthodontic surgery were enrolled. 3D CT images were reconstructed, and 14 landmarks were identified on the model surface. Ten linear and four angle measurements were calculated using these landmarks. Homologous ramus models were constructed for each sample, and after converting all homologous models to the right side, 30 homologous models of the ramus were analysed using principal component analysis. Firstly, eight principal components explained >80% of the total variance. Differences between the deviated and contralateral sides in measurements and scores of the eight principal components were tested. Significant difference at the 5% level between the deviated and contralateral sides was observed in five linear measurements, three angle measurements and the third principal component. The variance of the deviated side was significantly larger in the diameter between the mandibular notch and coronoid process, horizontal dilated angle of the mandibular ramus and vertical dilated angle of the mandibular ramus. The variance of the contralateral side was significantly larger in the height of mandibular ramus, height of posterior of mandibular ramus, condylar width, height of condylar head and mandibular angle. The squared multiple correlation coefficient adjusted for the degrees of freedom was 0.815. The third principal

  2. A Practical Guide to Molecular Docking and Homology Modelling for Medicinal Chemists.

    Science.gov (United States)

    Lohning, Anna E; Levonis, Stephan M; Williams-Noonan, Billy; Schweiker, Stephanie S

    2017-01-01

    Elucidating details of the relationship between molecular structure and a particular biological end point is essential for successful, rational drug discovery. Molecular docking is a widely accepted tool for lead identification however, navigating the intricacies of the software can be daunting. Our objective was therefore to provide a step-by-step guide for those interested in incorporating contemporary basic molecular docking and homology modelling into their design strategy. Three molecular docking programs, AutoDock4, SwissDock and Surflex-Dock, were compared in the context of a case study where a set of steroidal and non-steroidal ligands were docked into the human androgen receptor (hAR) using both rigid and flexible target atoms. Metrics for comparison included how well each program predicted the X-ray structure orientation via root mean square deviation (rmsd), predicting known actives via ligand ranking and comparison to biological data where available. Benchmarking metrics were discussed in terms of identifying accurate and reliable results. For cases where no three dimensional structure exists, we provided a practical example for creating a homology model using Swiss-Model. Results showed an rmsd between X-ray ligands from wild-type and mutant receptors and docked poses were 4.15Å and 0.83Å (SwissDock), 2.69Å and 8.80Å (AutoDock4) and 0.39Å and 0.71Å (Surflex-Dock) respectively. Surflex-Dock performed consistently well in pose prediction (less than 2Å) while Auto- Dock4 predicted known active non-steroidal antiandrogens most accurately. Introducing flexibility into target atoms produced the largest degree of change in ligand ranking in Surflex-Dock. We produced a viable homology model of the P2X1 purireceptor for subsequent docking analysis. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  3. Three-dimensional homology model of GlcNAc-TV glycosyltransferase.

    Science.gov (United States)

    Janoš, Pavel; Kozmon, Stanislav; Tvaroška, Igor; Koca, Jaroslav

    2016-07-01

    The enzyme UDP-N-acetylglucosamine: α-d-mannoside β-1-6 N-acetylglucosaminyltransferase V (GnT-V) catalyzes the transfer of GlcNAc from the UDP-GlcNAc donor to the α-1-6-linked mannose of the trimannosyl core structure of glycoproteins to produce the β-1-6-linked branching of N-linked oligosaccharides. β-1-6-GlcNAc-branched N-glycans are associated with cancer growth and metastasis. Therefore, the inhibition of GnT-V represents a key target for anti-cancer drug development. However, the development of potent and specific inhibitors of GnT-V is hampered by the lack of information on the three-dimensional structure of the enzyme and on the binding characteristics of its substrates. Here we present the first 3D structure of GnT-V as a result of homology modeling. Various alignment methods, docking the donor and acceptor substrates, and molecular dynamics simulation were used to construct seven homology models of GnT-V and characterize the binding of its substrates. The best homology model is consistent with available experimental data. The three-dimensional model, the structure of the enzyme catalytic site and binding information obtained for the donor and acceptor can be useful in studies of the catalytic mechanism and design of inhibitors of GnT-V. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. The theory of networks of single server queues and the tandem queue model

    Directory of Open Access Journals (Sweden)

    Pierre Le Gall

    1997-01-01

    Full Text Available We consider the stochastic behavior of networks of single server queues when successive service times of a given customer are highly correlated. The study is conducted in two particular cases: 1 networks in heavy traffic, and 2 networks in which all successive service times have the same value (for a given customer, in order to avoid the possibility of breaking up the busy periods. We then show how the local queueing delay (for an arbitrary customer can be derived through an equivalent tandem queue on the condition that one other local queueing delay is added: the jitter delay due to the independence of partial traffic streams.

  5. Structural insights into Saccharomyces cerevisiae Msh4-Msh5 complex function using homology modeling.

    Directory of Open Access Journals (Sweden)

    Ramaswamy Rakshambikai

    Full Text Available The Msh4-Msh5 protein complex in eukaryotes is involved in stabilizing Holliday junctions and its progenitors to facilitate crossing over during Meiosis I. These functions of the Msh4-Msh5 complex are essential for proper chromosomal segregation during the first meiotic division. The Msh4/5 proteins are homologous to the bacterial mismatch repair protein MutS and other MutS homologs (Msh2, Msh3, Msh6. Saccharomyces cerevisiae msh4/5 point mutants were identified recently that show two fold reduction in crossing over, compared to wild-type without affecting chromosome segregation. Three distinct classes of msh4/5 point mutations could be sorted based on their meiotic phenotypes. These include msh4/5 mutations that have a crossover and viability defects similar to msh4/5 null mutants; b intermediate defects in crossing over and viability and c defects only in crossing over. The absence of a crystal structure for the Msh4-Msh5 complex has hindered an understanding of the structural aspects of Msh4-Msh5 function as well as molecular explanation for the meiotic defects observed in msh4/5 mutations. To address this problem, we generated a structural model of the S. cerevisiae Msh4-Msh5 complex using homology modeling. Further, structural analysis tailored with evolutionary information is used to predict sites with potentially critical roles in Msh4-Msh5 complex formation, DNA binding and to explain asymmetry within the Msh4-Msh5 complex. We also provide a structural rationale for the meiotic defects observed in the msh4/5 point mutations. The mutations are likely to affect stability of the Msh4/5 proteins and/or interactions with DNA. The Msh4-Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation.

  6. Gclust Server: 97794 [Gclust Server

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    Full Text Available 97794 CEL_B0244.2_25143920 Cluster Sequences Related Sequences(171) 767 ida-1: related to Islet cell Diabete...ida-1: related to Islet cell Diabetes Autoantigen family member (ida-1) Number of Sequences 1 Homologs 1 Clu

  7. Gclust Server: 5789 [Gclust Server

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    Full Text Available of alpha-cells, binds to Aga1p during agglutination, N-terminal half is homologous to the immunoglobulin su...nces(341) Sequence length 650 Representative annotation Alpha-agglutinin of alpha-cells, binds to Aga1p during agglutination

  8. Gclust Server: 200669 [Gclust Server

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    Full Text Available 200669 Bsu_BSU06890=cotJA Cluster Sequences - 82 polypeptide composition of the spo...k to cluster sequences Cluster Sequences Link to related sequences - Sequence length 82 Representative annotation polypeptide composi...tion of the spore coat Number of Sequences 1 Homologs 1

  9. Gclust Server: 177066 [Gclust Server

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    Full Text Available 177066 Bsu_BSU06900=cotJB Cluster Sequences - 100 polypeptide composition of the sp...nk to cluster sequences Cluster Sequences Link to related sequences - Sequence length 100 Representative annotation polypeptide compo...sition of the spore coat Number of Sequences 1 Homologs

  10. Gclust Server: 116907 [Gclust Server

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    Full Text Available osis receptor inducing membrane injury gene ; no annotation 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 116907 ...4.1 pro-oncosis receptor inducing membrane injury gene ; no annotation Number of Sequences 1 Homologs 1 Clus

  11. Gclust Server: 43604 [Gclust Server

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    Full Text Available 43604 CEL_Y71F9AL.18_17510487 Cluster Sequences Related Sequences(51) 945 pme-1: Poly(ADP-ribose) Metabolism...equences Related Sequences(51) Sequence length 945 Representative annotation pme-1: Poly(ADP-ribose) Metab...olism Enzyme family member (pme-1) Number of Sequences 2 Homologs 2 Clustering thre

  12. Gclust Server: 96223 [Gclust Server

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    Full Text Available alpha-glucosidase (sucrase-maltase-isomaltase) 1 1.00e-28 0.0 0.0 0.0 0.0 3.23 0.0 Show 96223 Cluster ID 962...ha-glucosidase (sucrase-maltase-isomaltase) Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-28 P

  13. Gclust Server: 112838 [Gclust Server

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    Full Text Available XERODERMA PIGMENTOSUM COMPLEMENTATION GROUP B 1); ATP-dependent helicase 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.... (ARABIDOPSIS HOMOLOG OF XERODERMA PIGMENTOSUM COMPLEMENTATION GROUP B 1); ATP-dependent helicase Number of

  14. Gclust Server: 112883 [Gclust Server

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    Full Text Available XERODERMA PIGMENTOSUM COMPLEMENTATION GROUP B 2); ATP-dependent helicase 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.... (ARABIDOPSIS HOMOLOG OF XERODERMA PIGMENTOSUM COMPLEMENTATION GROUP B 2); ATP-dependent helicase Number of

  15. Gclust Server: 581 [Gclust Server

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    Full Text Available 581 HSA_4507709 Cluster Sequences Related Sequences(506) 321 NP_003304.1 tissue specific transplantation...elated Sequences(506) Sequence length 321 Representative annotation NP_003304.1 tissue specific transplant...ation antigen P35B ; no annotation Number of Sequences 97 Homologs 97 Clustering th

  16. Gclust Server: 85750 [Gclust Server

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    Full Text Available 54448_165; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7s...pecies) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 11.11 Cyanobacteria (25species) (%)

  17. Gclust Server: 111286 [Gclust Server

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    Full Text Available species) (%) 0.0 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 11.11 Cyanobacteria (25species) (%)...254670_127; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-45 Plants and algae (7

  18. Gclust Server: 26348 [Gclust Server

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    Full Text Available localized protein that protects membranes from desiccation 4 1.00e-28 0.0 0.0 0.0 0.0 0.0 50.0 Show 26348 Cl...membrane localized protein that protects membranes from desiccation Number of Sequences 4 Homologs 4 Cluster

  19. Gclust Server: 116379 [Gclust Server

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    Full Text Available IVE PROTEIN PRECURSOR PIRG (CELL SURFACE PROTEIN) (EXP53) 1 1.00e-99 0.0 0.0 0.0 0.0 3.23 0.0 Show 116379 Cl...D REPETITIVE PROTEIN PRECURSOR PIRG (CELL SURFACE PROTEIN) (EXP53) Number of Sequences 1 Homologs 1 Clusteri

  20. Gclust Server: 13693 [Gclust Server

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    Full Text Available 13693 HSA_72534784 Cluster Sequences Related Sequences(7) 379 NP_001026915.1 RIB43A domain with coiled-coils...1 RIB43A domain with coiled-coils 1 isoform 1 ; no annotation Number of Sequences 8 Homologs 8 Clustering th

  1. Gclust Server: 243 [Gclust Server

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    Full Text Available 243 CEL_K07E3.3_17568735 Cluster Sequences Related Sequences(40) 303 dao-3: Dauer or Aging adult Over...o-3: Dauer or Aging adult Overexpression family member (dao-3) Number of Sequences 142 Homologs 142 Clusteri

  2. Gclust Server: 191579 [Gclust Server

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    Full Text Available 191579 DME_CG15288_24584296 Cluster Sequences - 3375 wb: wing blister CG15288-PB, i...Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 3375 Representative annotation wb: wing blist...er CG15288-PB, isoform B Number of Sequences 1 Homologs

  3. Gclust Server: 203470 [Gclust Server

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    Full Text Available 203470 DME_CG15288_24584298 Cluster Sequences - 2731 wb: wing blister CG15288-PA, i...Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 2731 Representative annotation wb: wing blist...er CG15288-PA, isoform A Number of Sequences 1 Homologs

  4. Gclust Server: 68976 [Gclust Server

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    Full Text Available transporter component involved in competition for nodulation 1 1.00e-45 0.0 0.0 0.0 0.0 3.23 0.0 Show 68976 ...tative ABC transporter component involved in competition for nodulation Number of Sequences 1 Homologs 1 Clu

  5. Gclust Server: 145558 [Gclust Server

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    Full Text Available 145558 DME_CG4399_24639236 Cluster Sequences - 2301 east: enhanced adult sensory threshold...ntative annotation east: enhanced adult sensory threshold CG4399-PB Number of Seq...uences 1 Homologs 1 Clustering threshold 1.00e+00 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromal

  6. Gclust Server: 11283 [Gclust Server

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    Full Text Available eshold 9.98e-01 Plants and algae (7species) (%) 42.86 Other Bikonts (Chromalveolata... Representative annotation estExt_Genewise1_v1.C_LG_IV1489 Number of Sequences 9 Homologs 9 Clustering thr

  7. Gclust Server: 201480 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 201480 SCE_YHR214C-E Cluster Sequences - 99 Identified by gene-trapping, microarray...-based expression analysis, and genome-wide homology searching 1 1.00e-50 0.0 0.0 0.0 0.0 0.0 12.5 Show 201480 Cluster ID 2014

  8. Gclust Server: 150578 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 150578 DME_CG14472_17352461 Cluster Sequences - 5322 poe: purity of essence CG14472...to cluster sequences Cluster Sequences Link to related sequences - Sequence length 5322 Representative annotation poe: purity of esse...nce CG14472-PA Number of Sequences 1 Homologs 1 Clusteri

  9. Gclust Server: 64440 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available to Flo1p, thought to be expressed and involved in flocculation 1 1.00e+00 0.0 0.0 0.0 0.0 0.0 12.5 Show 644...ith similarity to Flo1p, thought to be expressed and involved in flocculation Number of Sequences 1 Homologs

  10. Gclust Server: 201383 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 201383 SCE_YHR214C-D Cluster Sequences - 97 Identified by gene-trapping, microarray...-based expression analysis, and genome-wide homology searching 1 1.00e-45 0.0 0.0 0.0 0.0 0.0 12.5 Show 201383 Cluster ID 2013

  11. Gclust Server: 20137 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 20137 HSA_5803017 Cluster Sequences Related Sequences(29) 338 NP_006723.1 FBJ murin...e osteosarcoma viral oncogene homolog B ; no annotation 5 1.00e-35 0.0 0.0 0.0 0.0 0.0 25.0 Show 20137 Cluster ID 2013

  12. Gclust Server: 51304 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 136 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(3) Sequence length 185 Representative...umber of Sequences 2 Homologs 2 Clustering threshold 1.00e-80 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  13. Gclust Server: 73643 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available e length 1927 Representative annotation fgenesh1_pg.C_scaffold_323000002; no anno...tation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-10 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  14. Gclust Server: 109449 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 1971 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(71) Sequence length 372 Representative...Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  15. Gclust Server: 70345 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available nk to cluster sequences Cluster Sequences Link to related sequences Related Sequences(502) Sequence length 603 Representative...uences 1 Homologs 1 Clustering threshold 1.00e-45 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  16. Gclust Server: 66041 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 66041 Rpal_RPA0109 Cluster Sequences Related Sequences(968) 262 putative 3-oxoacyl-...nce length 262 Representative annotation putative 3-oxoacyl-(acyl carrier ptn) re...ductase Number of Sequences 1 Homologs 1 Clustering threshold 9.98e-01 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  17. Gclust Server: 75971 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 45551469 Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 386 Representative...Sequences 1 Homologs 1 Clustering threshold 1.00e+00 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  18. Gclust Server: 107030 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 2235 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(91) Sequence length 250 Representative...Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 14.29 Other Bikonts (Chromalve

  19. Gclust Server: 32 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 3989 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(507) Sequence length 254 Representative...n Number of Sequences 411 Homologs 411 Clustering threshold 1.00e-45 Plants and algae (7species) (%) 28.57 Other Bikonts (Chromalve

  20. Gclust Server: 105676 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 3073 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(105) Sequence length 529 Representative...mber of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 14.29 Other Bikonts (Chromalve

  1. Gclust Server: 100527 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available nown function, expression is induced during nitrogen limitation 1 9.98e-01 0.0 0.0 0.0 0.0 0.0 12.5 Show 100... Protein of unknown function, expression is induced during nitrogen limitation Number of Sequences 1 Homolog

  2. Gclust Server: 88311 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available the expression of genes during nutrient limitation 1 1.00e+00 0.0 0.0 0.0 0.0 0.0 12.5 Show 88311 Cluster ID... the expression of genes during nutrient limitation Number of Sequences 1 Homologs 1 Clustering threshold 1.

  3. Gclust Server: 4312 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available yltransferase, forming alpha-glycosyl linkages protein 24 1.00e-45 0.0 0.0 40.0 40.0 12.9 0.0 Show 4312 Clus... glycosyltransferase, forming alpha-glycosyl linkages protein Number of Sequences 24 Homologs 24 Clustering

  4. Gclust Server: 102057 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ike protein that localizes to the shmoo tip (mating projection) 1 1.00e+00 0.0 0.0 0.0 0.0 0.0 12.5 Show 102...b1p ubiquitin-like protein that localizes to the shmoo tip (mating projection) Number of Sequences 1 Homolog

  5. Gclust Server: 95736 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available e [Agrobacterium tumefaciens str. C58 (U. Washington)] 1 1.00e-40 0.0 0.0 4.0 0.0 0.0 0.0 Show 95736 Cluster...etase [Agrobacterium tumefaciens str. C58 (U. Washington)] Number of Sequences 1 Homologs 1 Clustering thres

  6. Gclust Server: 92828 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 92828 Sep_SE1644 Cluster Sequences Related Sequences(243) 416 probabale ammonium tr...ster sequences Cluster Sequences Link to related sequences Related Sequences(243) Sequence length 416 Repres...entative annotation probabale ammonium transporter Number of Sequences 1 Homologs

  7. Gclust Server: 93256 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 93256 Ana_all2643 Cluster Sequences Related Sequences(206) 1102 microcystin synthet... sequences Cluster Sequences Link to related sequences Related Sequences(206) Sequence length 1102 Representative annotation microcys...tin synthetase B Number of Sequences 1 Homologs 1 Cluste

  8. Gclust Server: 5459 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 5459 HSA_59806357 Cluster Sequences Related Sequences(355) 134 NP_036522.3 submaxillary...notation NP_036522.3 submaxillary gland androgen regulated protein 3 homolog A precursor ; no annotation Num...to related sequences Related Sequences(355) Sequence length 134 Representative an

  9. Gclust Server: 2893 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 2893 Syn_sll1596 Cluster Sequences Related Sequences(5) 108 circadian rhythm protei...equences Cluster Sequences Link to related sequences Related Sequences(5) Sequence length 108 Representative annotation circadian rhy...thm protein Number of Sequences 33 Homologs 33 Clusterin

  10. Gclust Server: 128685 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 128685 Rpa4_RPB_1544 Cluster Sequences Related Sequences(7) 201 Generic methyltrans...luster sequences Cluster Sequences Link to related sequences Related Sequences(7) Sequence length 201 Representative annotation Gener...ic methyltransferase Number of Sequences 1 Homologs 1 Cl

  11. Gclust Server: 133246 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 133246 Rpa4_RPB_1538 Cluster Sequences Related Sequences(3) 238 Generic methyltrans...luster sequences Cluster Sequences Link to related sequences Related Sequences(3) Sequence length 238 Representative annotation Gener...ic methyltransferase Number of Sequences 1 Homologs 1 Cl

  12. Gclust Server: 203310 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 203310 Bja_bll2067=nfeC Cluster Sequences - 275 nodulate formation efficiency C pro...ciency C protein Number of Sequences 1 Homologs 1 Cluste...cluster sequences Cluster Sequences Link to related sequences - Sequence length 275 Representative annotation nodulate formation effi

  13. Gclust Server: 77761 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 77761 CEL_C52E4.4_17563248 Cluster Sequences Related Sequences(327) 435 rpt-1: proteasome Regulatory Particl... rpt-1: proteasome Regulatory Particle, ATPase-like family member (rpt-1) Number of Sequences 1 Homologs 1 C

  14. Gclust Server: 71012 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 71012 CEL_F23F1.8_71987364 Cluster Sequences Related Sequences(458) 406 rpt-4: proteasome Regulatory Particl... rpt-4: proteasome Regulatory Particle, ATPase-like family member (rpt-4) Number of Sequences 1 Homologs 1 C

  15. Gclust Server: 71014 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 71014 CEL_F23F1.8_71987372 Cluster Sequences Related Sequences(458) 398 rpt-4: proteasome Regulatory Particl... rpt-4: proteasome Regulatory Particle, ATPase-like family member (rpt-4) Number of Sequences 1 Homologs 1 C

  16. Gclust Server: 94171 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available Subunit of Signal Recognition Particleno annotation 1 9.98e-01 14.29 0.0 0.0 0.0 0.0 0.0 Show 94171 Cluster ...54 Subunit of Signal Recognition Particleno annotation Number of Sequences 1 Homologs 1 Clustering threshold

  17. Gclust Server: 2653 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 2653 CEL_F23F12.6_17554784 Cluster Sequences Related Sequences(106) 414 rpt-3: proteasome Regulatory Particl...tion rpt-3: proteasome Regulatory Particle, ATPase-like family member (rpt-3) Number of Sequences 35 Homolog

  18. Gclust Server: 101440 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available vacuolar protein, required for wild-type resistance to vanadate 1 1.00e-12 0.0 0.0 0.0 0.0 0.0 12.5 Show 101... Cell wall and vacuolar protein, required for wild-type resistance to vanadate Number of Sequences 1 Homolog

  19. Gclust Server: 75573 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ed translocation partner in lipoma ; no annotation 1 1.00e+00 0.0 0.0 0.0 0.0 0.0 12.5 Show 75573 Cluster ID...red translocation partner in lipoma ; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.

  20. Gclust Server: 150703 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available MPT63/MPB63) (16 kDa IMMUNOPROTECTIVE EXTRACELLULAR PROTEIN) 1 1.00e-80 0.0 0.0 0.0 0.0 3.23 0.0 Show 15070...PT63 (ANTIGEN MPT63/MPB63) (16 kDa IMMUNOPROTECTIVE EXTRACELLULAR PROTEIN) Number of Sequences 1 Homologs 1

  1. Gclust Server: 38578 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 38578 SCE_YMR059W=SEN15 Cluster Sequences - 148 Subunit of the tRNA splicing endonuclease, which is composed...licing endonuclease, which is composed of Sen2p, Sen15p, Sen34p, and Sen54p Number of Sequences 3 Homologs 3

  2. Gclust Server: 129348 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 129348 TET_1545.m00002 Cluster Sequences Related Sequences(6) 113 REGULATOR OF CHROMOSOME CONDENSATION...ENSATION-related chr_0_8254899_1545; no annotation Number of Sequences 1 Homologs 1... sequences Related Sequences(6) Sequence length 113 Representative annotation REGULATOR OF CHROMOSOME COND

  3. Gclust Server: 82033 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ponent, nuclear pre-mRNA splicing factorno annotation 1 1.00e-16 14.29 0.0 0.0 0.0 0.0 0.0 Show 82033 Cluste...e Component, nuclear pre-mRNA splicing factorno annotation Number of Sequences 1 Homologs 1 Clustering thres

  4. Gclust Server: 35345 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ent of the Swr1p complex that incorporates Htz1p into chromatin 3 1.00e-60 0.0 0.0 0.0 0.0 0.0 37.5 Show 353...nction, component of the Swr1p complex that incorporates Htz1p into chromatin Number of Sequences 3 Homologs

  5. Gclust Server: 35549 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available nt of the Swr1p complex that incorporates Htz1p into chromatin 3 1.00e-60 0.0 0.0 0.0 0.0 0.0 37.5 Show 3554...tion, component of the Swr1p complex that incorporates Htz1p into chromatin Number of Sequences 3 Homologs 3

  6. Gclust Server: 32232 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 32232 CEL_T23G7.4_17536427 Cluster Sequences Related Sequences(14) 884 sec-5: yeast... SEC homolog family member (sec-5) 3 1.00e-90 0.0 0.0 0.0 0.0 0.0 37.5 Show 32232 Cluster ID 32232 Sequence

  7. Gclust Server: 9682 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available TED: similar to Fatty acid-binding protein, epidermal (E-FABP) (Psoriasis-associated fatty acid-binding prot...r to Fatty acid-binding protein, epidermal (E-FABP) (Psoriasis-associated fatty acid-binding protein homolog

  8. Gclust Server: 137655 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available dentified by expression profiling and mass spectrometry 1 1.00e-16 0.0 0.0 0.0 0.0 0.0 12.5 Show 137655 Clus...tion, identified by expression profiling and mass spectrometry Number of Sequences 1 Homologs 1 Clustering t

  9. Gclust Server: 138873 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available dentified by expression profiling and mass spectrometry 1 1.00e-31 0.0 0.0 0.0 0.0 0.0 12.5 Show 138873 Clus...tion, identified by expression profiling and mass spectrometry Number of Sequences 1 Homologs 1 Clustering t

  10. Gclust Server: 66489 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available se, coupled to transmembrane movement of substances 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 66489 Cluster ...TPase, coupled to transmembrane movement of substances Number of Sequences 1 Homologs 1 Clustering threshold

  11. Gclust Server: 75497 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ase, coupled to transmembrane movement of substances 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 75497 Cluster... ATPase, coupled to transmembrane movement of substances Number of Sequences 1 Homologs 1 Clustering thresho

  12. Gclust Server: 66247 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available se, coupled to transmembrane movement of substances 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 66247 Cluster ...TPase, coupled to transmembrane movement of substances Number of Sequences 1 Homologs 1 Clustering threshold

  13. Gclust Server: 66827 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available Pase, coupled to transmembrane movement of substances 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 66827 Cluste...); ATPase, coupled to transmembrane movement of substances Number of Sequences 1 Homologs 1 Clustering thres

  14. Gclust Server: 75217 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available e, coupled to transmembrane movement of substances 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 75217 Cluster I...ase, coupled to transmembrane movement of substances Number of Sequences 1 Homologs 1 Clustering threshold 1

  15. Gclust Server: 6147 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available coupled to transmembrane movement of substances 17 1.00e-99 57.14 11.11 0.0 0.0 0.0 0.0 Show 6147 Cluster ID... coupled to transmembrane movement of substances Number of Sequences 17 Homologs 17 Clustering threshold 1.0

  16. Gclust Server: 111116 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 111116 ATH_AT3G20370_18402593 Cluster Sequences - 379 meprin and TRAF homology doma...in-containing protein / MATH domain-containing protein 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 111116 Cluster ID 11111

  17. Microwave accelerated synthesis of isoxazole hydrazide inhibitors of the system xc- transporter: Initial homology model.

    Science.gov (United States)

    Matti, Afnan A; Mirzaei, Joseph; Rudolph, John; Smith, Stephen A; Newell, Jayme L; Patel, Sarjubhai A; Braden, Michael R; Bridges, Richard J; Natale, Nicholas R

    2013-11-01

    Microwave accelerated reaction system (MARS) technology provided a good method to obtain selective and open isoxazole ligands that bind to and inhibit the Sxc- antiporter. The MARS provided numerous advantages, including: shorter time, better yield and higher purity of the product. Of the newly synthesized series of isoxazoles the salicyl hydrazide 6 exhibited the highest level of inhibitory activity in the transport assay. A homology model has been developed to summarize the SAR results to date, and provide a working hypothesis for future studies.

  18. Expression,Purification,Characteristics and Homology Modeling of the HMGS from Streptococcus pneumoniae

    Institute of Scientific and Technical Information of China (English)

    YA-LI BEN; GU-ZHEN CUI; CHEN LI; RUI HAN; JIE ZHANG; QING-YE ZHANG; JIAN WAN; DE-LI LIU

    2009-01-01

    Objective To understand the molecular basis for a potential reaction mechanism and develop novel antibiotics with homology modeling for 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase (HMGS). Methods The genetic engineering technology and the composer module of SYBYL7.0 program were used,while the HMGS three-dimensional structure was analyzed by homology modeling. Results The mvaS gene was cloned from Streptococcus pneumoniae and overexpressed in Escherichia coli from a pET28 vector.The expressed enzyme (about 46 kDa) was purified by affinity chromatography with a specific activity of 3.24 μmol/min/mg.Optimal conditions were pH 9.75 and 10 mmol/L MgCl2 at 37℃.The Vmax and Km were 4.69 μmol/mirdmg and 213 μmol/L respectively.The 3D model of S.pneumoniae HMGS was established based on structure template of HMGS of Enterococcus faecalis. Conclusion The structure of HMGS will facilitate the structure-based design of alternative drugs to cholesterol-lowering therapies or to novel antibiotics to the Gram-positive cocci,whereas the recombinant HMGS will prove useful for drug development against a different enzyme in the mevalonate pathway.

  19. Improved homology model of cyclohexanone monooxygenase from Acinetobacter calcoaceticus based on multiple templates.

    Science.gov (United States)

    Bermúdez, Eduardo; Ventura, Oscar N; Eriksson, Leif A; Saenz-Méndez, Patricia

    2014-04-01

    A new homology model of cyclohexanone monooxygenase (CHMO) from Acinetobacter calcoaceticus is derived based on multiple templates, and in particular the crystal structure of CHMO from Rhodococcus sp. The derived model was fully evaluated, showing that the quality of the new structure was improved over previous models. Critically, the nicotinamide cofactor is included in the model for the first time. Analysis of several molecular dynamics snapshots of intermediates in the enzymatic mechanism led to a description of key residues for cofactor binding and intermediate stabilization during the reaction, in particular Arg327 and the well known conserved motif (FxGxxxHxxxW) in Baeyer-Villiger monooxygenases, in excellent agreement with known experimental and computational data.

  20. An active site homology model of phenylalanine ammonia-lyase from Petroselinum crispum.

    Science.gov (United States)

    Röther, Dagmar; Poppe, László; Morlock, Gaby; Viergutz, Sandra; Rétey, János

    2002-06-01

    The plant enzyme phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) shows homology to histidine ammonia-lyase (HAL) whose structure has been solved by X-ray crystallography. Based on amino-acid sequence alignment of the two enzymes, mutagenesis was performed on amino-acid residues that were identical or similar to the active site residues in HAL to gain insight into the importance of this residues in PAL for substrate binding or catalysis. We mutated the following amino-acid residues: S203, R354, Y110, Y351, N260, Q348, F400, Q488 and L138. Determination of the kinetic constants of the overexpressed and purified enzymes revealed that mutagenesis led in each case to diminished activity. Mutants S203A, R354A and Y351F showed a decrease in kcat by factors of 435, 130 and 235, respectively. Mutants F400A, Q488A and L138H showed a 345-, 615- and 14-fold lower kcat, respectively. The greatest loss of activity occurred in the PAL mutants N260A, Q348A and Y110F, which were 2700, 2370 and 75 000 times less active than wild-type PAL. To elucidate the possible function of the mutated amino-acid residues in PAL we built a homology model of PAL based on structural data of HAL and mutagenesis experiments with PAL. The homology model of PAL showed that the active site of PAL resembles the active site of HAL. This allowed us to propose possible roles for the corresponding residues in PAL catalysis.

  1. A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

    Directory of Open Access Journals (Sweden)

    Maurer Till

    2005-04-01

    Full Text Available Abstract Background We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350. The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS. Results To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ. The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms. Conclusion In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

  2. Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations

    Directory of Open Access Journals (Sweden)

    Simonson Thomas

    2008-10-01

    Full Text Available Abstract Background Structure-based computational methods are needed to help identify and characterize protein-protein complexes and their function. For individual proteins, the most successful technique is homology modelling. We investigate a simple extension of this technique to protein-protein complexes. We consider a large set of complexes of known structures, involving pairs of single-domain proteins. The complexes are compared with each other to establish their sequence and structural similarities and the relation between the two. Compared to earlier studies, a simpler dataset, a simpler structural alignment procedure, and an additional energy criterion are used. Next, we compare the Xray structures to models obtained by threading the native sequence onto other, homologous complexes. An elementary requirement for a successful energy function is to rank the native structure above any threaded structure. We use the DFIREβ energy function, whose quality and complexity are typical of the models used today. Finally, we compare near-native models to distinctly non-native models. Results If weakly stable complexes are excluded (defined by a binding energy cutoff, as well as a few unusual complexes, a simple homology principle holds: complexes that share more than 35% sequence identity share similar structures and interaction modes; this principle was less clearcut in earlier studies. The energy function was then tested for its ability to identify experimental structures among sets of decoys, produced by a simple threading procedure. On average, the experimental structure is ranked above 92% of the alternate structures. Thus, discrimination of the native structure is good but not perfect. The discrimination of near-native structures is fair. Typically, a single, alternate, non-native binding mode exists that has a native-like energy. Some of the associated failures may correspond to genuine, alternate binding modes and/or native complexes that

  3. Equipment for fully homologous bulb turbine model testing in Laval University

    Science.gov (United States)

    R, Fraser; D, Vallée; Y, Jean; C, Deschênes

    2014-03-01

    Within the context of liberalisation of the energy market, hydroelectricity remains a first class source of clean and renewable energy. Combining the growing demand of energy, its increasing value and the appreciation associated to the sustainable development, low head sites formerly considered as non-profitable are now exploitable. Bulb turbines likely to equip such sites are traditionally developed on model using right angle transmission leading to piers enlargement for power take off shaft passage, thus restricting possibilities to have fully homologous hydraulic passages. Aiming to sustain good quality development on fully homologous scale model of bulb turbines, the Hydraulic Machines Laboratory (LAMH) of Laval University has developed a brake with an enhanced power to weight ratio. This powerful brake is small enough to be located in the bulb shell while dissipating power without mandatory test head reduction. This paper first presents the basic technology of this brake and its application. Then both its main performance capabilities and dimensional characteristics will be detailed. The instrumentation used to perform accurate measurements will be finally presented.

  4. Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode.

    Science.gov (United States)

    Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

    2017-05-07

    Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS-SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening

    Energy Technology Data Exchange (ETDEWEB)

    Kalyanaraman, C.; Imker, H; Fedorov, A; Fedorov, E; Glasner, M; Babbitt, P; Almo, S; Gerlt, J; Jacobson, M

    2008-01-01

    We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.

  6. Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes

    DEFF Research Database (Denmark)

    Terp, G E; Christensen, I T; Jørgensen, Flemming Steen

    2000-01-01

    Matrix metalloproteinases are extracellular enzymes taking part in the remodeling of extracellular matrix. The structures of the catalytic domain of MMP1, MMP3, MMP7 and MMP8 are known, but structures of enzymes belonging to this family still remain to be determined. A general approach...... to the homology modeling of matrix metalloproteinases, exemplified by the modeling of MMP2, MMP9, MMP12 and MMP14 is described. The models were refined using an energy minimization procedure developed for matrix metalloproteinases. This procedure includes incorporation of parameters for zinc and calcium ions...... in the AMBER 4.1 force field, applying a non-bonded approach and a full ion charge representation. Energy minimization of the apoenzymes yielded structures with distorted active sites, while reliable three-dimensional structures of the enzymes containing a substrate in active site were obtained. The structural...

  7. Gclust Server: 83577 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available Suppressor of Mec and Unc defects family member (smu-2) Number of Sequences 1 Homologs 1 Clustering threshol...pressor of Mec and Unc defects family member (smu-2) 1 1.00e-35 0.0 0.0 0.0 0.0 0.0 12.5 Show 83577 Cluster ...83577 CEL_Y49F6B.4_17535725 Cluster Sequences Related Sequences(243) 547 smu-2: Sup

  8. Gclust Server: 157070 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 157070 NCR_NCU00271 Cluster Sequences - 138 predicted protein (translation) (139 aa...); no annotation 1 1.00e-70 0.0 0.0 0.0 0.0 0.0 12.5 Show 157070 Cluster ID 157070 Sequence ID NCR_NCU00271 ...nces 1 Homologs 1 Clustering threshold 1.00e-70 Plants and algae (7species) (%) 0.0 Other Bikonts (Chromalve

  9. Gclust Server: 14093 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available trin domain with coiled-coils 1 NSP5a3a ; no annotation 7 1.00e-99 0.0 0.0 0.0 0.0 0.0 25.0 Show 14093 Clust...1 spectrin domain with coiled-coils 1 NSP5a3a ; no annotation Number of Sequences 7 Homologs 7 Clustering th

  10. Gclust Server: 183670 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ng histone to protamine replacement) ; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1...lacement) ; no annotation 1 1.00e-70 0.0 0.0 0.0 0.0 0.0 12.5 Show 183670 Cluster I...183670 HSA_4885635 Cluster Sequences - 138 NP_005416.1 transition protein 2 (during histone to protamine rep...uence length 138 Representative annotation NP_005416.1 transition protein 2 (duri

  11. Gclust Server: 148576 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ear migration, localizes to the mother cell cortex and the bud tip Number of Sequences 1 Homologs 1 Clusteri...tion, localizes to the mother cell cortex and the bud tip 1 1.00e+00 0.0 0.0 0.0 0.0 0.0 12.5 Show 148576 Cl...148576 SCE_YDR150W=NUM1 Cluster Sequences - 2748 Protein required for nuclear migra

  12. Gclust Server: 2779 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ion clu-1: yeast CLU (mitochondrial clustering) related family member (clu-1) Number of Sequences 34 Homolog...2779 CEL_F55H2.6_17552758 Cluster Sequences Related Sequences(87) 1247 clu-1: yeast CLU (mitochondrial clust...ering) related family member (clu-1) 34 1.00e-80 71.43 66.67 0.0 0.0 0.0 50.0 Show

  13. Gclust Server: 26038 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 5.2 protein 7 transactivated by hepatitis B virus X antigen ; no annotation Number of Sequences 4 Homologs 4...26038 HSA_29788776 Cluster Sequences Related Sequences(3) 409 NP_612635.2 protein 7 transactivated by hepati...tis B virus X antigen ; no annotation 4 1.00e-22 0.0 0.0 0.0 0.0 0.0 12.5 Show 2603

  14. Gclust Server: 31458 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 129992.1 PREDICTED: similar to plasticity-related protein 2 ; no annotation Number of Sequences 3 Homologs 3...31458 HSA_113428395 Cluster Sequences Related Sequences(35) 698 XP_001129992.1 PREDICTED: similar to plastic...ity-related protein 2 ; no annotation 3 1.00e-28 0.0 0.0 0.0 0.0 0.0 12.5 Show 3145

  15. Gclust Server: 184210 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ion, identified based on comparison to related yeast species Number of Sequences 1 Homologs 1 Clustering thr...184210 SCE_YJL052C-A Cluster Sequences - 39 Putative protein of unknown function, identified based on compar...ison to related yeast species 1 1.00e-14 0.0 0.0 0.0 0.0 0.0 12.5 Show 184210 Clust

  16. Gclust Server: 190190 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 190190 Sco_SCO0112 Cluster Sequences - 51 hypothetical protein 1 1.00e-19 0.0 0.0 0.0 0.0 3.23 0.0 Show 19...0190 Cluster ID 190190 Sequence ID Sco_SCO0112 Link to cluster sequences Cluster Sequ...f Sequences 1 Homologs 1 Clustering threshold 1.00e-19 Plants and algae (7species

  17. Gclust Server: 19198 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 19198 DPTM_GSPATP00004359001 Cluster Sequences Related Sequences(324) 635 no annotation 5 1.00e-19... 0.0 22.22 4.0 0.0 0.0 0.0 Show 19198 Cluster ID 19198 Sequence ID DPTM_GSPATP00004359001 Lin...5 Representative annotation no annotation Number of Sequences 5 Homologs 5 Clustering threshold 1.00e-19

  18. Gclust Server: 71162 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available on rpt-6: proteasome Regulatory Particle, ATPase-like family member (rpt-6) Number of Sequences 1 Homologs 1...71162 CEL_Y49E10.1_17554786 Cluster Sequences Related Sequences(437) 416 rpt-6: proteasome Regulatory Partic...le, ATPase-like family member (rpt-6) 1 1.00e-60 0.0 0.0 0.0 0.0 0.0 12.5 Show 7116

  19. Gclust Server: 107931 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available A20-binding inhibitor of NF-kappaB activation 2 ; no annotation Number of Sequences 1 Homologs 1 Clustering...107931 HSA_34147370 Cluster Sequences Related Sequences(83) 429 NP_077285.2 A20-binding inhibitor of NF-kapp...aB activation 2 ; no annotation 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 107931 Clu

  20. Gclust Server: 95647 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available SE DEHYDROGENASE (D-THREO ALDOSE 1-DEHYDROGENASE) PROTEIN Number of Sequences 1 Homologs 1 Clustering thresh...EHYDROGENASE (D-THREO ALDOSE 1-DEHYDROGENASE) PROTEIN 1 9.98e-01 0.0 0.0 0.0 0.0 3.23 0.0 Show 95647 Cluster...95647 Sme_SMc02775 Cluster Sequences Related Sequences(219) 339 PUTATIVE L-FUCOSE D

  1. Data Mining Model for the Data Retrieval from Central Server Configuration

    Directory of Open Access Journals (Sweden)

    Srivatsan Sridharan

    2013-10-01

    Full Text Available A server, which is to keep track of heavy document traffic, is unable to filter the documents that are mostrelevant and updated for continuous text search queries. This paper focuses on handling continuous textextraction sustaining high document traffic. The main objective is to retrieve recent updated documentsthat are most relevant to the query by applying sliding window technique. Our solution indexes thestreamed documents in the main memory with structure based on the principles of inverted file, andprocesses document arrival and expiration events with incremental threshold-based method. It also ensureselimination of duplicate document retrieval using unsupervised duplicate detection. The documents areranked based on user feedback and given higher priority for retrieval.

  2. Tumor necrosis factor alpha of teleosts: in silico characterization and homology modeling

    Directory of Open Access Journals (Sweden)

    Tran Ngoc Tuan

    2016-10-01

    Full Text Available Tumor necrosis factor alpha (TNF- is known to be crucial in many biological activities of organisms. In this study, physicochemical properties and modeling of TNF- protein of fish was analyzed using in silico approach. TNF- proteins selected from fish species, including grass carp (Ctenopharyngodon idella, zebra fish (Danio rerio, Nile tilapia (Oreochromis niloticus, goldfish (Carassius auratus, and rainbow trout (Oncorhynchus mykiss were used in this study. Physicochemical characteristics with molecular weight, theoretical isoelectric point, extinction coefficient, aliphatic index, instability index, total number of negatively charged residues and positively charged residues, and grand average of hydropathicity were computed. All proteins were classified as transmembrane proteins. The “transmembrane region” and “TNF” domain were identified from protein sequences. The function prediction of proteins was also performed. Alpha helices and random coils were dominating in the secondary structure of the proteins. Three-dimensional structures were predicted and verified as good structures for the investigation of TNF- of fish by online server validation.

  3. Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality

    Science.gov (United States)

    Jacunski, Alexandra; Dixon, Scott J.; Tatonetti, Nicholas P.

    2015-01-01

    Synthetic lethality is a genetic interaction wherein two otherwise nonessential genes cause cellular inviability when knocked out simultaneously. Drugs can mimic genetic knock-out effects; therefore, our understanding of promiscuous drugs, polypharmacology-related adverse drug reactions, and multi-drug therapies, especially cancer combination therapy, may be informed by a deeper understanding of synthetic lethality. However, the colossal experimental burden in humans necessitates in silico methods to guide the identification of synthetic lethal pairs. Here, we present SINaTRA (Species-INdependent TRAnslation), a network-based methodology that discovers genome-wide synthetic lethality in translation between species. SINaTRA uses connectivity homology, defined as biological connectivity patterns that persist across species, to identify synthetic lethal pairs. Importantly, our approach does not rely on genetic homology or structural and functional similarity, and it significantly outperforms models utilizing these data. We validate SINaTRA by predicting synthetic lethality in S. pombe using S. cerevisiae data, then identify over one million putative human synthetic lethal pairs to guide experimental approaches. We highlight the translational applications of our algorithm for drug discovery by identifying clusters of genes significantly enriched for single- and multi-drug cancer therapies. PMID:26451775

  4. Discovery of Entamoeba histolytica hexokinase 1 inhibitors through homology modeling and virtual screening.

    Science.gov (United States)

    Saucedo-Mendiola, María Leticia; Salas-Pacheco, José Manuel; Nájera, Hugo; Rojo-Domínguez, Arturo; Yépez-Mulia, Lilián; Avitia-Domínguez, Claudia; Téllez-Valencia, Alfredo

    2014-06-01

    Entamoeba histolytica, the parasite which causes amebiasis is responsible for 110,000 deaths a year. Entamoeba histolytica depends on glycolysis to obtain ATP for cellular work. According to metabolic flux studies, hexokinase exerts the highest flux control of this metabolic pathway; therefore, it is an excellent target in the search of new antiamebic drugs. To this end, a tridimensional model of E. histolytica hexokinase 1 (EhHK1) was constructed and validated by homology modeling. After virtual screening of 14,400 small molecules, the 100 with the best docking scores were selected, purchased and assessed in their inhibitory capacity. The results showed that three molecules (compounds 2921, 11275 and 2755) inhibited EhHK1 with an I50 of 48, 91 and 96 µM, respectively. Thus, we found the first inhibitors of EhHK1 that can be used in the search of new chemotherapeutic agents against amebiasis.

  5. Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model.

    Science.gov (United States)

    Evers, Andreas; Klebe, Gerhard

    2004-10-21

    The neurokinin-1 (NK1) receptor belongs to the family of G-protein-coupled receptors (GPCRs), which represents one of the most relevant target families in small-molecule drug design. In this paper, we describe a homology modeling of the NK1 receptor based on the high-resolution X-ray structure of rhodopsin and the successful virtual screening based on this protein model. The NK1 receptor model has been generated using our new MOBILE (modeling binding sites including ligand information explicitly) approach. Starting with preliminary homology models, it generates improved models of the protein binding pocket together with bound ligands. Ligand information is used as an integral part in the homology modeling process. For the construction of the NK1 receptor, antagonist CP-96345 was used to restrain the modeling. The quality of the obtained model was validated by probing its ability to accommodate additional known NK1 antagonists from structurally diverse classes. On the basis of the generated model and on the analysis of known NK1 antagonists, a pharmacophore model was deduced, which subsequently guided the 2D and 3D database search with UNITY. As a following step, the remaining hits were docked into the modeled binding pocket of the NK1 receptor. Finally, seven compounds were selected for biochemical testing, from which one showed affinity in the submicromolar range. Our results suggest that ligand-supported homology models of GPCRs may be used as effective platforms for structure-based drug design.

  6. Insights to ligand binding to the monoamine transporters – from homology modeling to LeuBAT and dDAT

    Directory of Open Access Journals (Sweden)

    Heidi eKoldsø

    2015-09-01

    Full Text Available Understanding of drug binding to the human biogenic amine transporters is essential to explain the mechanism of action of these pharmaceuticals but more importantly to be able to develop new and improved compounds to be used in the treatment of depression or drug addiction. Until recently no high resolution structure was available of the biogenic amine transporters and homology modeling was a necessity. Various studies have revealed experimentally validated binding modes of numerous ligands to the biogenic amine transporters using homology modeling. Here we examine and discuss the similarities between the binding models of substrates, antidepressants, psychostimulants and anti-abuse drugs in homology models of the human biogenic amine transporters and the recently published crystal structures of the drosophila dopamine transporter and the engineered protein, LeuBAT. The comparison reveals that careful computational modeling combined with experimental data can be utilized to predict binding of molecules to proteins that agree very well with crystal structures.

  7. Insights to ligand binding to the monoamine transporters—from homology modeling to LeuBAT and dDAT

    Science.gov (United States)

    Koldsø, Heidi; Grouleff, Julie; Schiøtt, Birgit

    2015-01-01

    Understanding of drug binding to the human biogenic amine transporters (BATs) is essential to explain the mechanism of action of these pharmaceuticals but more importantly to be able to develop new and improved compounds to be used in the treatment of depression or drug addiction. Until recently no high resolution structure was available of the BATs and homology modeling was a necessity. Various studies have revealed experimentally validated binding modes of numerous ligands to the BATs using homology modeling. Here we examine and discuss the similarities between the binding models of substrates, antidepressants, psychostimulants, and mazindol in homology models of the human BATs and the recently published crystal structures of the Drosophila dopamine transporter and the engineered protein, LeuBAT. The comparison reveals that careful computational modeling combined with experimental data can be utilized to predict binding of molecules to proteins that agree very well with crystal structures. PMID:26441663

  8. Multiple conformational states in retrospective virtual screening - homology models vs. crystal structures: beta-2 adrenergic receptor case study.

    Science.gov (United States)

    Mordalski, Stefan; Witek, Jagna; Smusz, Sabina; Rataj, Krzysztof; Bojarski, Andrzej J

    2015-01-01

    Distinguishing active from inactive compounds is one of the crucial problems of molecular docking, especially in the context of virtual screening experiments. The randomization of poses and the natural flexibility of the protein make this discrimination even harder. Some of the recent approaches to post-docking analysis use an ensemble of receptor models to mimic this naturally occurring conformational diversity. However, the optimal number of receptor conformations is yet to be determined. In this study, we compare the results of a retrospective screening of beta-2 adrenergic receptor ligands performed on both the ensemble of receptor conformations extracted from ten available crystal structures and an equal number of homology models. Additional analysis was also performed for homology models with up to 20 receptor conformations considered. The docking results were encoded into the Structural Interaction Fingerprints and were automatically analyzed by support vector machine. The use of homology models in such virtual screening application was proved to be superior in comparison to crystal structures. Additionally, increasing the number of receptor conformational states led to enhanced effectiveness of active vs. inactive compounds discrimination. For virtual screening purposes, the use of homology models was found to be most beneficial, even in the presence of crystallographic data regarding the conformational space of the receptor. The results also showed that increasing the number of receptors considered improves the effectiveness of identifying active compounds by machine learning methods. Graphical abstractComparison of machine learning results obtained for various number of beta-2 AR homology models and crystal structures.

  9. Earth System Model Development and Analysis using FRE-Curator and Live Access Servers: On-demand analysis of climate model output with data provenance.

    Science.gov (United States)

    Radhakrishnan, A.; Balaji, V.; Schweitzer, R.; Nikonov, S.; O'Brien, K.; Vahlenkamp, H.; Burger, E. F.

    2016-12-01

    There are distinct phases in the development cycle of an Earth system model. During the model development phase, scientists make changes to code and parameters and require rapid access to results for evaluation. During the production phase, scientists may make an ensemble of runs with different settings, and produce large quantities of output, that must be further analyzed and quality controlled for scientific papers and submission to international projects such as the Climate Model Intercomparison Project (CMIP). During this phase, provenance is a key concern:being able to track back from outputs to inputs. We will discuss one of the paths taken at GFDL in delivering tools across this lifecycle, offering on-demand analysis of data by integrating the use of GFDL's in-house FRE-Curator, Unidata's THREDDS and NOAA PMEL's Live Access Servers (LAS).Experience over this lifecycle suggests that a major difficulty in developing analysis capabilities is only partially the scientific content, but often devoted to answering the questions "where is the data?" and "how do I get to it?". "FRE-Curator" is the name of a database-centric paradigm used at NOAA GFDL to ingest information about the model runs into an RDBMS (Curator database). The components of FRE-Curator are integrated into Flexible Runtime Environment workflow and can be invoked during climate model simulation. The front end to FRE-Curator, known as the Model Development Database Interface (MDBI) provides an in-house web-based access to GFDL experiments: metadata, analysis output and more. In order to provide on-demand visualization, MDBI uses Live Access Servers which is a highly configurable web server designed to provide flexible access to geo-referenced scientific data, that makes use of OPeNDAP. Model output saved in GFDL's tape archive, the size of the database and experiments, continuous model development initiatives with more dynamic configurations add complexity and challenges in providing an on

  10. Gclust Server: 2566 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 2566 ATH_AT4G23100_15236390 Cluster Sequences Related Sequences(2) 522 RML1 (PHYTOALEXIN DEFICIE...notation RML1 (PHYTOALEXIN DEFICIENT 2, ROOT MERISTEMLESS 1); glutamate-cysteine ligase Number of Sequences ...36 Homologs 36 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 85.71 Other Bikonts (Chromalveolata, Excavata) (9specie...s) (%) 0.0 Cyanobacteria (25species) (%) 0.0 Photosynthetic bacteria (15specie...s) (%) 60.0 Non-photosynthetic bacteria (31species) (%) 45.16 Opisthokonts (Animals and fungi) (8specie

  11. Gclust Server: 80061 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 80061 ATH_AT1G52340_15218213 Cluster Sequences Related Sequences(316) 285 ABA2 (ABA DEFICIE...s(316) Sequence length 285 Representative annotation ABA2 (ABA DEFICIENT 2); oxid...oreductase Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-28 Plants and algae (7species) (%) 14....29 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 0.0 Photosynthetic bacteria (15specie...s) (%) 0.0 Non-photosynthetic bacteria (31species) (%) 0.0

  12. Gclust Server: 107862 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 107862 ATH_AT1G16540_18394375 Cluster Sequences - 819 ABA3/ATABA3/LOS5/SIR3 (ABA DEFICIE...ces 1 Homologs 1 Clustering threshold 1.00e+00 Plants and algae (7species) (%) 14.29 Other Bikonts (Chromalv...eolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 0.0 Photosynthetic bacteria (15specie...s) (%) 0.0 Non-photosynthetic bacteria (31species) (%) 0.0 Opisthokonts (Animals and fungi) (8specie...s) (%) 0.0 Number of Sequences for each species ATH: 1 Species not appearing in this cluster

  13. Gclust Server: 42331 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available /BHLH029/FIT1/FRU (FE-DEFICIENCY INDUCED TRANSCRIPTION FACTOR 1); DNA binding / transcription factor 2 1.00e...uence length 318 Representative annotation ATBHLH029/BHLH029/FIT1/FRU (FE-DEFICIENCY INDUCED TRANSCRIPTION F...ACTOR 1); DNA binding / transcription factor Number of Sequences 2 Homologs 2 Clustering threshold 1.00e-12 Plants and algae (7specie...s) (%) 28.57 Other Bikonts (Chromalveolata, Excavata) (9specie...s) (%) 0.0 Cyanobacteria (25species) (%) 0.0 Photosynthetic bacteria (15species) (%) 0.0 Non-photosynthetic bacteria (31specie

  14. Gclust Server: 70506 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 70506 ATH_AT3G53130_42565881 Cluster Sequences Related Sequences(500) 539 LUT1 (LUTEIN DEFICIE...nces(500) Sequence length 539 Representative annotation LUT1 (LUTEIN DEFICIENT 1)...; oxygen binding Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-35 Plants and algae (7species) ...(%) 14.29 Other Bikonts (Chromalveolata, Excavata) (9species) (%) 0.0 Cyanobacteria (25species) (%) 0.0 Phot...osynthetic bacteria (15species) (%) 0.0 Non-photosynthetic bacteria (31species) (

  15. Gclust Server: 143424 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available ired for survival upon exposure to K1 killer toxin Number of Sequences 1 Homologs 1 Clustering threshold 1.0...osure to K1 killer toxin 1 1.00e-70 0.0 0.0 0.0 0.0 0.0 12.5 Show 143424 Cluster ID...143424 SCE_YOR183W=FYV12 Cluster Sequences - 129 Protein of unknown function, required for survival upon exp...- Sequence length 129 Representative annotation Protein of unknown function, requ

  16. Gclust Server: 47677 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available in shmoo formation and bipolar bud site selection 2 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 47677 Cluster ID ...in shmoo formation and bipolar bud site selection Number of Sequences 2 Homologs 2 Clustering threshold 1.00...47677 SCE_YLR313C=SPH1 Cluster Sequences Related Sequences(5) 661 Protein involved ...ated Sequences(5) Sequence length 661 Representative annotation Protein involved

  17. Gclust Server: 90952 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available Minization of XX and XO animals family member (fem-2) Number of Sequences 1 Homologs 1 Clustering threshold ...90952 CEL_T19C3.8_17553792 Cluster Sequences Related Sequences(251) 449 fem-2: FEMinization of XX and XO ani...mals family member (fem-2) 1 1.00e-28 0.0 0.0 0.0 0.0 0.0 12.5 Show 90952 Cluster I...es Related Sequences(251) Sequence length 449 Representative annotation fem-2: FE

  18. Gclust Server: 69953 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 69953 Eco_b4003=zraS Cluster Sequences Related Sequences(529) 465 sensory histidine... kinase in two-component regulatory system with ZraR 1 1.00e-25 0.0 0.0 0.0 0.0 3.23 0.0 Show 69953 Cluster ...ID 69953 Sequence ID Eco_b4003=zraS Link to cluster sequences Cluster Sequences Link to related sequences Re...ine kinase in two-component regulatory system with ZraR Number of Sequences 1 Homologs 1 Clustering threshol

  19. Gclust Server: 191007 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available lacement) ; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.0...acement) ; no annotation 1 1.00e-25 0.0 0.0 0.0 0.0 0.0 12.5 Show 191007 Cluster ID...191007 HSA_4507629 Cluster Sequences - 55 NP_003275.1 transition protein 1 (during histone to protamine repl...ence length 55 Representative annotation NP_003275.1 transition protein 1 (during histone to protamine rep

  20. Gclust Server: 118602 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 118602 CEL_Y39E4B.8_17556857 Cluster Sequences Related Sequences(27) 268 zig-8: 2 (...Zwei) IG-domain protein family member (zig-8) 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 118602 Cluster ID 118...Related Sequences(27) Sequence length 268 Representative annotation zig-8: 2 (Zwe...i) IG-domain protein family member (zig-8) Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Pl

  1. Gclust Server: 121488 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 121488 CEL_Y48A6A.1_71994240 Cluster Sequences Related Sequences(19) 260 zig-5: 2 (...Zwei) IG-domain protein family member (zig-5) 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 121488 Cluster ID 121...Related Sequences(19) Sequence length 260 Representative annotation zig-5: 2 (Zwe...i) IG-domain protein family member (zig-5) Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Pl

  2. Gclust Server: 145821 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available sted, animals roll when moving family member (rol-3) Number of Sequences 1 Homologs 1 Clustering threshold 1...145821 CEL_C16D9.2_32566642 Cluster Sequences - 2456 rol-3: ROLler: helically twisted, animals roll when mov...ing family member (rol-3) 1 1.00e+00 0.0 0.0 0.0 0.0 0.0 12.5 Show 145821 Cluster I...ces - Sequence length 2456 Representative annotation rol-3: ROLler: helically twi

  3. Gclust Server: 127772 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available harynx and Intestine in Excess family member (pie-1) Number of Sequences 1 Homologs 1 Clustering threshold 1...127772 CEL_Y49E10.14_17556058 Cluster Sequences Related Sequences(7) 335 pie-1: Pharynx and Intestine in Exc...ess family member (pie-1) 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 127772 Cluster I...ences Related Sequences(7) Sequence length 335 Representative annotation pie-1: P

  4. Gclust Server: 3559 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 3559 Cch_Cag_1017 Cluster Sequences Related Sequences(11) 312 HhH-GPD 28 1.00e-50 7...1.43 33.33 0.0 33.33 6.45 75.0 Show 3559 Cluster ID 3559 Sequence ID Cch_Cag_1017 Link to cluster sequences Clus...ion HhH-GPD Number of Sequences 28 Homologs 28 Clustering threshold 1.00e-50 Plan...: 1 SCE: 1 DCGR: 1 DKLA: 1 NCR: 1 TET: 1 NGR: 1 HSA: 8 DME: 1 Species not appearing in this cluster OSA: 0 O

  5. Gclust Server: 151690 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available brane protein that binds to and inhibits GTP-bound Ras2p at the ER Number of Sequences 1 Homologs 1 Clusteri...tein that binds to and inhibits GTP-bound Ras2p at the ER 1 1.00e-35 0.0 0.0 0.0 0.0 0.0 12.5 Show 151690 Cl...151690 SCE_YPL096C-A=ERI1 Cluster Sequences - 68 Endoplasmic reticulum membrane pro

  6. Gclust Server: 13096 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 13096 CEL_Y54E10A.4_71995469 Cluster Sequences Related Sequences(22) 405 fog-1: Fem...inization Of Germline family member (fog-1) 8 1.00e-99 0.0 0.0 0.0 0.0 0.0 37.5 Show 13096 Cluster ID 13096 ...ated Sequences(22) Sequence length 405 Representative annotation fog-1: Feminizat...ion Of Germline family member (fog-1) Number of Sequences 8 Homologs 8 Clustering threshold 1.00e-99 Plants

  7. Gclust Server: 83402 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 83402 DME_CG3650_24762751 Cluster Sequences Related Sequences(288) 249 CG3650: CG36...50-PA 1 1.00e-07 0.0 0.0 0.0 0.0 0.0 12.5 Show 83402 Cluster ID 83402 Sequence ID DME_CG3650_24762751 Link to cluster sequences Clus...epresentative annotation CG3650: CG3650-PA Number of Sequences 1 Homologs 1 Clust....5 Number of Sequences for each species DME: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 P

  8. Gclust Server: 162002 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 162002 Mlo_mlr6313 Cluster Sequences - 108 hypothetical protein 1 1.00e-50 0.0 0.0 ...0.0 0.0 3.23 0.0 Show 162002 Cluster ID 162002 Sequence ID Mlo_mlr6313 Link to cluster sequences Cluster Seq... of Sequences 1 Homologs 1 Clustering threshold 1.00e-50 Plants and algae (7speci...ecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  9. Gclust Server: 26711 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 26711 DPTM_GSPATP00019280001 Cluster Sequences Related Sequences(1) 146 no annotati...on 4 1.00e-60 0.0 11.11 0.0 0.0 0.0 0.0 Show 26711 Cluster ID 26711 Sequence ID DPTM_GSPATP00019280001 Link to clus...presentative annotation no annotation Number of Sequences 4 Homologs 4 Clustering...umber of Sequences for each species DPTM: 4 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT:

  10. Gclust Server: 196605 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 196605 OTAU_34323 Cluster Sequences - 129 0800010210 1 1.00e-60 14.29 0.0 0.0 0.0 0.0 0.0 Show 196605 Clus...ter ID 196605 Sequence ID OTAU_34323 Link to cluster sequences Cluster Sequences Link... to related sequences - Sequence length 129 Representative annotation 0800010210 Number of Sequences 1 Homologs 1 Clus...ecies) (%) 0.0 Number of Sequences for each species OTAU: 1 Species not appearing in this clus

  11. Gclust Server: 204043 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 204043 Sme_SMa0535 Cluster Sequences - 57 hypothetical protein 1 1.00e-22 0.0 0.0 0....0 0.0 3.23 0.0 Show 204043 Cluster ID 204043 Sequence ID Sme_SMa0535 Link to cluster sequences Cluster Sequ...f Sequences 1 Homologs 1 Clustering threshold 1.00e-22 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  12. Gclust Server: 194603 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 194603 Rde_RD1_0095 Cluster Sequences - 95 hypothetical protein 1 1.00e-45 0.0 0.0 ...0.0 6.67 0.0 0.0 Show 194603 Cluster ID 194603 Sequence ID Rde_RD1_0095 Link to cluster sequences Cluster Se... of Sequences 1 Homologs 1 Clustering threshold 1.00e-45 Plants and algae (7speci...ecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  13. Gclust Server: 15827 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 15827 DPTM_GSPATP00001608001 Cluster Sequences Related Sequences(1) 146 no annotati...on 7 1.00e-28 0.0 11.11 0.0 0.0 0.0 0.0 Show 15827 Cluster ID 15827 Sequence ID DPTM_GSPATP00001608001 Link to clus...presentative annotation no annotation Number of Sequences 7 Homologs 7 Clustering...umber of Sequences for each species DPTM: 7 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT:

  14. Gclust Server: 69884 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 69884 PHRA_74081 Cluster Sequences - 942 fgenesh1_pg.C_scaffold_6000064; no annotat...ion 1 1.00e+00 0.0 11.11 0.0 0.0 0.0 0.0 Show 69884 Cluster ID 69884 Sequence ID PHRA_74081 Link to cluster sequences Clus...h1_pg.C_scaffold_6000064; no annotation Number of Sequences 1 Homologs 1 Clusteri... Number of Sequences for each species PHRA: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PP

  15. Gclust Server: 118003 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 118003 Sco_SCO6323 Cluster Sequences Related Sequences(30) 218 tetR-family regulato...ry protein 1 1.00e-12 0.0 0.0 0.0 0.0 3.23 0.0 Show 118003 Cluster ID 118003 Sequence ID Sco_SCO6323 Link to cluster sequences Clus...resentative annotation tetR-family regulatory protein Number of Sequences 1 Homologs 1 Clus...cies) (%) 0.0 Number of Sequences for each species Sco: 1 Species not appearing in this cluster ATH: 0 OSA:

  16. Gclust Server: 154667 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 154667 Hal_VNG1895H Cluster Sequences - 115 hypothetical protein 1 1.00e-60 0.0 0.0... 0.0 0.0 3.23 0.0 Show 154667 Cluster ID 154667 Sequence ID Hal_VNG1895H Link to cluster sequences Cluster S...er of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and algae (7spe...Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR:

  17. Gclust Server: 125119 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 125119 Sto_ST1658 Cluster Sequences Related Sequences(6) 890 hypothetical protein 1... 1.00e-99 0.0 0.0 0.0 0.0 3.23 0.0 Show 125119 Cluster ID 125119 Sequence ID Sto_ST1658 Link to cluster sequences Clus...notation hypothetical protein Number of Sequences 1 Homologs 1 Clustering thresho...Sequences for each species Sto: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0

  18. Gclust Server: 163001 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 163001 Mac_MA3296 Cluster Sequences - 154 hypothetical protein 1 1.00e-80 0.0 0.0 0....0 0.0 3.23 0.0 Show 163001 Cluster ID 163001 Sequence ID Mac_MA3296 Link to cluster sequences Cluster Seque...f Sequences 1 Homologs 1 Clustering threshold 1.00e-80 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  19. Gclust Server: 84016 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 84016 OSA_Os02g0670900@1 Cluster Sequences Related Sequences(282) 422 no annotation... 1 1.00e-40 14.29 0.0 0.0 0.0 0.0 0.0 Show 84016 Cluster ID 84016 Sequence ID OSA_Os02g0670900@1 Link to cluster sequences Clus...entative annotation no annotation Number of Sequences 1 Homologs 1 Clustering thr...r of Sequences for each species OSA: 1 Species not appearing in this cluster ATH: 0 PoTR: 0 PPT: 0 CRE: 0 OT

  20. Gclust Server: 109780 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 109780 DPTM_GSPATP00005450001 Cluster Sequences Related Sequences(70) 613 no annota...tion 1 1.00e-10 0.0 11.11 0.0 0.0 0.0 0.0 Show 109780 Cluster ID 109780 Sequence ID DPTM_GSPATP00005450001 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(70) Sequence length 6...13 Representative annotation no annotation Number of Sequences 1 Homologs 1 Clust...0.0 Number of Sequences for each species DPTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0

  1. Gclust Server: 43062 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 43062 PoTR_776385 Cluster Sequences Related Sequences(82) 560 fgenesh4_pg.C_LG_XV00...0813 2 1.00e-50 28.57 0.0 0.0 0.0 0.0 0.0 Show 43062 Cluster ID 43062 Sequence ID PoTR_776385 Link to cluster sequences Clus...tive annotation fgenesh4_pg.C_LG_XV000813 Number of Sequences 2 Homologs 2 Cluste....0 Number of Sequences for each species OSA: 1 PoTR: 1 Species not appearing in this cluster ATH: 0 PPT: 0 C

  2. Gclust Server: 140712 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 140712 PPT_79340 Cluster Sequences - 345 fgenesh1_pg.scaffold_78000050; no annotati...on 1 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 140712 Cluster ID 140712 Sequence ID PPT_79340 Link to cluster sequences Clus...h1_pg.scaffold_78000050; no annotation Number of Sequences 1 Homologs 1 Clusterin...Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE:

  3. Gclust Server: 984 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 984 PoTR_290599 Cluster Sequences Related Sequences(105) 158 gw1.5132.5.1 74 1.00e-...25 14.29 0.0 0.0 66.67 51.61 0.0 Show 984 Cluster ID 984 Sequence ID PoTR_290599 Link to cluster sequences Clus...ion gw1.5132.5.1 Number of Sequences 74 Homologs 74 Clustering threshold 1.00e-25...2 Species not appearing in this cluster ATH: 0 OSA: 0 PPT: 0 CRE: 0 OTAU: 0 CME:

  4. Gclust Server: 113527 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 113527 DPTM_GSPATP00011034001 Cluster Sequences - 545 no annotation 1 1.00e+00 0.0 ...11.11 0.0 0.0 0.0 0.0 Show 113527 Cluster ID 113527 Sequence ID DPTM_GSPATP00011034001 Link to cluster sequences Clus...on Number of Sequences 1 Homologs 1 Clustering threshold 1.00e+00 Plants and alga... DPTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA

  5. Gclust Server: 158898 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 158898 TET_435.m00013 Cluster Sequences - 23 hypothetical protein chr_0_8253807_435...; no annotation 1 1.00e-06 0.0 11.11 0.0 0.0 0.0 0.0 Show 158898 Cluster ID 158898 Sequence ID TET_435.m00013 Link to clus...ter sequences Cluster Sequences Link to related sequences - Sequence length 23 Representative ...annotation hypothetical protein chr_0_8253807_435; no annotation Number of Sequences 1 Homologs 1 Clus...fungi) (8species) (%) 0.0 Number of Sequences for each species TET: 1 Species not appearing in this cluster

  6. Gclust Server: 175864 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 175864 PoTR_766696 Cluster Sequences - 334 fgenesh4_pg.C_LG_VIII001710 1 1.00e-99 1...4.29 0.0 0.0 0.0 0.0 0.0 Show 175864 Cluster ID 175864 Sequence ID PoTR_766696 Link to cluster sequences Clus...II001710 Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants an...pecies PoTR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA:

  7. Gclust Server: 147566 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 147566 Cvi_CV2421=prgJ Cluster Sequences - 100 cell invasion protein - cytoplasmic ...1 1.00e-45 0.0 0.0 0.0 0.0 3.23 0.0 Show 147566 Cluster ID 147566 Sequence ID Cvi_CV2421=prgJ Link to cluster sequences Clus... invasion protein - cytoplasmic Number of Sequences 1 Homologs 1 Clustering thres...f Sequences for each species Cvi: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE:

  8. Gclust Server: 146671 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 146671 Cvi_CV2161 Cluster Sequences - 203 hypothetical protein 1 1.00e-99 0.0 0.0 0....0 0.0 3.23 0.0 Show 146671 Cluster ID 146671 Sequence ID Cvi_CV2161 Link to cluster sequences Cluster Seque...f Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  9. Gclust Server: 11249 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 11249 DPTM_GSPATP00007539001 Cluster Sequences Related Sequences(159) 282 no annota...tion 9 1.00e-50 0.0 11.11 0.0 0.0 0.0 0.0 Show 11249 Cluster ID 11249 Sequence ID DPTM_GSPATP00007539001 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(159) Sequence length 28...2 Representative annotation no annotation Number of Sequences 9 Homologs 9 Cluste....0 Number of Sequences for each species DPTM: 9 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0

  10. Gclust Server: 67181 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 67181 OSA_Os01g0601200 Cluster Sequences Related Sequences(744) 345 no annotation 1... 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 67181 Cluster ID 67181 Sequence ID OSA_Os01g0601200 Link to cluster sequences Clus...tive annotation no annotation Number of Sequences 1 Homologs 1 Clustering thresho... Sequences for each species OSA: 1 Species not appearing in this cluster ATH: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU:

  11. Gclust Server: 193244 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 193244 CEL_C05C9.2_25152296 Cluster Sequences - 224 C05C9.2 1 1.00e-99 0.0 0.0 0.0 ...0.0 0.0 12.5 Show 193244 Cluster ID 193244 Sequence ID CEL_C05C9.2_25152296 Link to cluster sequences Cluste...r Sequences Link to related sequences - Sequence length 224 Representative annotation C05C9.2 Number of Sequences 1 Homologs 1 Clus...fungi) (8species) (%) 12.5 Number of Sequences for each species CEL: 1 Species not appearing in this clus

  12. Gclust Server: 142598 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 142598 OTAU_13235 Cluster Sequences - 158 fgenesh1_pg.C_Chr_13.0001000016 1 1.00e-8...0 14.29 0.0 0.0 0.0 0.0 0.0 Show 142598 Cluster ID 142598 Sequence ID OTAU_13235 Link to cluster sequences Clus..._13.0001000016 Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-80 Pla...each species OTAU: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 CME: 0 GTH: 0

  13. Gclust Server: 50879 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 50879 PHRA_95252 Cluster Sequences Related Sequences(1) 497 C_scaffold_35000036; no... annotation 2 1.00e-80 0.0 22.22 0.0 0.0 0.0 0.0 Show 50879 Cluster ID 50879 Sequence ID PHRA_95252 Link to cluster sequences Clus...sentative annotation C_scaffold_35000036; no annotation Number of Sequences 2 Homologs 2 Clus...species) (%) 0.0 Number of Sequences for each species PHRA: 1 PHSO: 1 Species not appearing in this cluster

  14. Gclust Server: 109809 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 109809 PoTR_576865 Cluster Sequences Related Sequences(70) 161 eugene3.00161000 1 1....00e-40 14.29 0.0 0.0 0.0 0.0 0.0 Show 109809 Cluster ID 109809 Sequence ID PoTR_576865 Link to cluster sequences Clus...nnotation eugene3.00161000 Number of Sequences 1 Homologs 1 Clustering threshold ...quences for each species PoTR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PPT: 0 CRE: 0 OTAU: 0 C

  15. Gclust Server: 185340 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 185340 Rpa1_RPE_4428 Cluster Sequences - 80 hypothetical protein 1 1.00e-35 0.0 0.0... 0.0 6.67 0.0 0.0 Show 185340 Cluster ID 185340 Sequence ID Rpa1_RPE_4428 Link to cluster sequences Cluster ...er of Sequences 1 Homologs 1 Clustering threshold 1.00e-35 Plants and algae (7spe... Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR:

  16. Gclust Server: 191350 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 191350 CEL_C12D8.13_71983663 Cluster Sequences - 244 C12D8.13 1 1.00e-99 0.0 0.0 0....0 0.0 0.0 12.5 Show 191350 Cluster ID 191350 Sequence ID CEL_C12D8.13_71983663 Link to cluster sequences Clus...Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) ...s not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS:

  17. Gclust Server: 203109 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 203109 Bja_bsr1885 Cluster Sequences - 92 hypothetical protein 1 1.00e-45 0.0 0.0 0....0 0.0 3.23 0.0 Show 203109 Cluster ID 203109 Sequence ID Bja_bsr1885 Link to cluster sequences Cluster Sequ...f Sequences 1 Homologs 1 Clustering threshold 1.00e-45 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  18. Gclust Server: 171077 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 171077 PPT_66313 Cluster Sequences - 140 fgenesh1_pg.scaffold_10000072; no annotati...on 1 1.00e-70 14.29 0.0 0.0 0.0 0.0 0.0 Show 171077 Cluster ID 171077 Sequence ID PPT_66313 Link to cluster sequences Clus...h1_pg.scaffold_10000072; no annotation Number of Sequences 1 Homologs 1 Clusterin...Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE:

  19. Gclust Server: 194588 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 194588 OSA_Os05g0554300 Cluster Sequences - 119 no annotation 1 1.00e-60 14.29 0.0 ...0.0 0.0 0.0 0.0 Show 194588 Cluster ID 194588 Sequence ID OSA_Os05g0554300 Link to cluster sequences Cluster... Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and algae (7species)...ies not appearing in this cluster ATH: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS: 0 Te

  20. Gclust Server: 199707 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 199707 PFA_PFD0925w Cluster Sequences - 277 hypothetical protein 1 1.00e-99 0.0 11....11 0.0 0.0 0.0 0.0 Show 199707 Cluster ID 199707 Sequence ID PFA_PFD0925w Link to cluster sequences Cluster ...ber of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7sp...1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PTR: 0 TPS

  1. Gclust Server: 169977 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 169977 PPT_97479 Cluster Sequences - 155 fgenesh1_pg.scaffold_326000015; no annotat...ion 1 1.00e-80 14.29 0.0 0.0 0.0 0.0 0.0 Show 169977 Cluster ID 169977 Sequence ID PPT_97479 Link to cluster sequences Clus...sh1_pg.scaffold_326000015; no annotation Number of Sequences 1 Homologs 1 Cluster...0 Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CR

  2. Gclust Server: 103700 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 103700 Mac_MA0620 Cluster Sequences Related Sequences(128) 674 sensory transduction... histidine kinase 1 1.00e-50 0.0 0.0 0.0 0.0 3.23 0.0 Show 103700 Cluster ID 103700 Sequence ID Mac_MA0620 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(128) Sequence length ...674 Representative annotation sensory transduction histidine kinase Number of Sequences 1 Homologs 1 Clus...d fungi) (8species) (%) 0.0 Number of Sequences for each species Mac: 1 Species not appearing in this cluste

  3. Gclust Server: 146590 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 146590 OSA_Os03g0800900 Cluster Sequences - 258 no annotation 1 1.00e-99 14.29 0.0 ...0.0 0.0 0.0 0.0 Show 146590 Cluster ID 146590 Sequence ID OSA_Os03g0800900 Link to cluster sequences Cluster... Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species)...ies not appearing in this cluster ATH: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS: 0 Te

  4. Gclust Server: 153222 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 153222 Mlo_msr8645 Cluster Sequences - 31 hypothetical protein 1 1.00e-10 0.0 0.0 0....0 0.0 3.23 0.0 Show 153222 Cluster ID 153222 Sequence ID Mlo_msr8645 Link to cluster sequences Cluster Sequ...f Sequences 1 Homologs 1 Clustering threshold 1.00e-10 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  5. Gclust Server: 195796 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 195796 PPT_96678 Cluster Sequences - 164 fgenesh1_pg.scaffold_309000014; no annotat...ion 1 1.00e-90 14.29 0.0 0.0 0.0 0.0 0.0 Show 195796 Cluster ID 195796 Sequence ID PPT_96678 Link to cluster sequences Clus...sh1_pg.scaffold_309000014; no annotation Number of Sequences 1 Homologs 1 Cluster...0 Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CR

  6. Gclust Server: 184275 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 184275 NGR_78246 Cluster Sequences - 446 estExt_fgeneshNG_pg.C_50054; no annotation... 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 184275 Cluster ID 184275 Sequence ID NGR_78246 Link to cluster sequences Clus...geneshNG_pg.C_50054; no annotation Number of Sequences 1 Homologs 1 Clustering th...er of Sequences for each species NGR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 C

  7. Gclust Server: 29806 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 29806 DPTM_GSPATP00032186001 Cluster Sequences Related Sequences(354) 329 no annota...tion 3 1.00e-50 0.0 11.11 0.0 0.0 0.0 0.0 Show 29806 Cluster ID 29806 Sequence ID DPTM_GSPATP00032186001 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(354) Sequence length 32...9 Representative annotation no annotation Number of Sequences 3 Homologs 3 Cluste....0 Number of Sequences for each species DPTM: 3 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0

  8. Gclust Server: 115507 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 115507 Mac_MA2993 Cluster Sequences Related Sequences(40) 130 hypothetical protein ...1 1.00e-70 0.0 0.0 0.0 0.0 3.23 0.0 Show 115507 Cluster ID 115507 Sequence ID Mac_MA2993 Link to cluster sequences Clus...annotation hypothetical protein Number of Sequences 1 Homologs 1 Clustering thres...f Sequences for each species Mac: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE:

  9. Gclust Server: 183951 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 183951 PHSO_142074 Cluster Sequences - 103 estExt_fgenesh1_pg.C_1080003; no annotat...ion 1 1.00e-50 0.0 11.11 0.0 0.0 0.0 0.0 Show 183951 Cluster ID 183951 Sequence ID PHSO_142074 Link to cluster sequences Clus...Ext_fgenesh1_pg.C_1080003; no annotation Number of Sequences 1 Homologs 1 Cluster...0 Number of Sequences for each species PHSO: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 P

  10. Gclust Server: 192795 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 192795 Eco_b1567=ydfW Cluster Sequences - 75 Qin prophage 1 1.00e-31 0.0 0.0 0.0 0....0 3.23 0.0 Show 192795 Cluster ID 192795 Sequence ID Eco_b1567=ydfW Link to cluster sequences Cluster Sequen...ces Link to related sequences - Sequence length 75 Representative annotation Qin prophage Number of Sequences 1 Homologs 1 Clus...gi) (8species) (%) 0.0 Number of Sequences for each species Eco: 1 Species not appearing in this clus

  11. Gclust Server: 53346 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 53346 PPT_96343 Cluster Sequences - 160 fgenesh1_pg.scaffold_300000056; no annotati...on 2 1.00e-90 14.29 0.0 0.0 0.0 0.0 0.0 Show 53346 Cluster ID 53346 Sequence ID PPT_96343 Link to cluster sequences Clus..._pg.scaffold_300000056; no annotation Number of Sequences 2 Homologs 2 Clustering...umber of Sequences for each species PPT: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE:

  12. Gclust Server: 150692 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 150692 PFA_PF14_0138 Cluster Sequences - 206 hypothetical protein 1 1.00e-99 0.0 11....11 0.0 0.0 0.0 0.0 Show 150692 Cluster ID 150692 Sequence ID PFA_PF14_0138 Link to cluster sequences Cluste...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7...: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PTR: 0 T

  13. Gclust Server: 120990 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 120990 OTAU_37391 Cluster Sequences Related Sequences(20) 430 1700010067 1 1.00e-99... 14.29 0.0 0.0 0.0 0.0 0.0 Show 120990 Cluster ID 120990 Sequence ID OTAU_37391 Link to cluster sequences Clus...n 1700010067 Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plant...ch species OTAU: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 CME: 0 GTH: 0 P

  14. Gclust Server: 159202 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 159202 PPT_98873 Cluster Sequences - 227 fgenesh1_pg.scaffold_370000022; no annotat...ion 1 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 159202 Cluster ID 159202 Sequence ID PPT_98873 Link to cluster sequences Clus...sh1_pg.scaffold_370000022; no annotation Number of Sequences 1 Homologs 1 Cluster...0 Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CR

  15. Gclust Server: 142563 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 142563 Pst_PSPTO_0354 Cluster Sequences - 52 hypothetical protein 1 1.00e-22 0.0 0....0 0.0 0.0 3.23 0.0 Show 142563 Cluster ID 142563 Sequence ID Pst_PSPTO_0354 Link to cluster sequences Cluste...mber of Sequences 1 Homologs 1 Clustering threshold 1.00e-22 Plants and algae (7s...1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR

  16. Gclust Server: 104109 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 104109 PHSO_141203 Cluster Sequences - 709 estExt_fgenesh1_pg.C_950051; no annotati...on 1 1.00e+00 0.0 11.11 0.0 0.0 0.0 0.0 Show 104109 Cluster ID 104109 Sequence ID PHSO_141203 Link to cluster sequences Clus...xt_fgenesh1_pg.C_950051; no annotation Number of Sequences 1 Homologs 1 Clusterin...Number of Sequences for each species PHSO: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT

  17. Gclust Server: 132995 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 132995 CRE_94549 Cluster Sequences Related Sequences(3) 93 no annotation 1 1.00e-40... 14.29 0.0 0.0 0.0 0.0 0.0 Show 132995 Cluster ID 132995 Sequence ID CRE_94549 Link to cluster sequences Clus...o annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-40 Plant...ch species CRE: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 OTAU: 0 CME: 0 GTH: 0 P

  18. Gclust Server: 89266 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 89266 DPTM_GSPATP00009171001 Cluster Sequences Related Sequences(234) 565 no annota...tion 1 1.00e-60 0.0 11.11 0.0 0.0 0.0 0.0 Show 89266 Cluster ID 89266 Sequence ID DPTM_GSPATP00009171001 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(234) Sequence length 56...5 Representative annotation no annotation Number of Sequences 1 Homologs 1 Cluste....0 Number of Sequences for each species DPTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0

  19. Gclust Server: 66269 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 66269 PPT_102988 Cluster Sequences - 697 fgenesh1_pg.scaffold_1009000001; no annota...tion 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 66269 Cluster ID 66269 Sequence ID PPT_102988 Link to cluster sequences Clus...sh1_pg.scaffold_1009000001; no annotation Number of Sequences 1 Homologs 1 Cluste....0 Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 C

  20. Gclust Server: 183148 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 183148 CME_CMA116C Cluster Sequences - 707 putative protein 1 1.00e-99 14.29 0.0 0....0 0.0 0.0 0.0 Show 183148 Cluster ID 183148 Sequence ID CME_CMA116C Link to cluster sequences Cluster Sequen...ces Link to related sequences - Sequence length 707 Representative annotation putative protein Number of Sequences 1 Homologs 1 Clus...nd fungi) (8species) (%) 0.0 Number of Sequences for each species CME: 1 Species

  1. Gclust Server: 46034 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 46034 OSA_Os09g0437500 Cluster Sequences Related Sequences(18) 146 no annotation 2 ...1.00e-70 28.57 0.0 0.0 0.0 0.0 0.0 Show 46034 Cluster ID 46034 Sequence ID OSA_Os09g0437500 Link to cluster sequences Clus...ve annotation no annotation Number of Sequences 2 Homologs 2 Clustering threshold...equences for each species OSA: 1 PoTR: 1 Species not appearing in this cluster ATH: 0 PPT: 0 CRE: 0 OTAU: 0

  2. Gclust Server: 71577 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 71577 Pm3_Pro1338=ftsH Cluster Sequences Related Sequences(461) 621 Cell division p...rotein FtsH 1 1.00e-28 0.0 0.0 4.0 0.0 0.0 0.0 Show 71577 Cluster ID 71577 Sequence ID Pm3_Pro1338=ftsH Link to clus... Representative annotation Cell division protein FtsH Number of Sequences 1 Homologs 1 Clus...ies) (%) 0.0 Number of Sequences for each species Pm3: 1 Species not appearing in this cluster ATH: 0 OSA: 0

  3. Gclust Server: 205769 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 205769 CEL_B0261.2_32563909 Cluster Sequences - 2692 kinase: B0261.2b 1 1.00e+00 0....0 0.0 0.0 0.0 0.0 12.5 Show 205769 Cluster ID 205769 Sequence ID CEL_B0261.2_32563909 Link to cluster sequences Clus...61.2b Number of Sequences 1 Homologs 1 Clustering threshold 1.00e+00 Plants and a...es CEL: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PF

  4. Gclust Server: 184334 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 184334 CEL_C05D9.9_17550162 Cluster Sequences - 93 C05D9.9 1 1.00e-45 0.0 0.0 0.0 0....0 0.0 12.5 Show 184334 Cluster ID 184334 Sequence ID CEL_C05D9.9_17550162 Link to cluster sequences Cluster... Sequences Link to related sequences - Sequence length 93 Representative annotation C05D9.9 Number of Sequences 1 Homologs 1 Clus...ngi) (8species) (%) 12.5 Number of Sequences for each species CEL: 1 Species not appearing in this clus

  5. Gclust Server: 157424 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 157424 CEL_F07C3.9_17559324 Cluster Sequences - 53 F07C3.9 1 1.00e-22 0.0 0.0 0.0 0....0 0.0 12.5 Show 157424 Cluster ID 157424 Sequence ID CEL_F07C3.9_17559324 Link to cluster sequences Cluster... Sequences Link to related sequences - Sequence length 53 Representative annotation F07C3.9 Number of Sequences 1 Homologs 1 Clus...ngi) (8species) (%) 12.5 Number of Sequences for each species CEL: 1 Species not appearing in this clus

  6. Gclust Server: 41327 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 41327 PoTR_677144 Cluster Sequences Related Sequences(221) 110 grail3.3299000301 2 ...1.00e-14 14.29 0.0 0.0 6.67 0.0 0.0 Show 41327 Cluster ID 41327 Sequence ID PoTR_677144 Link to cluster sequences Clus...annotation grail3.3299000301 Number of Sequences 2 Homologs 2 Clustering threshol... Sequences for each species PoTR: 1 Rpa2: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PPT: 0 CRE:

  7. Gclust Server: 118898 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 118898 DPTM_GSPATP00011796001 Cluster Sequences Related Sequences(26) 527 no annota...tion 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 118898 Cluster ID 118898 Sequence ID DPTM_GSPATP00011796001 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(26) Sequence length 5...27 Representative annotation no annotation Number of Sequences 1 Homologs 1 Clust...0.0 Number of Sequences for each species DPTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0

  8. Gclust Server: 107559 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 107559 CRE_147208 Cluster Sequences Related Sequences(86) 726 no annotation 1 1.00e...-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 107559 Cluster ID 107559 Sequence ID CRE_147208 Link to cluster sequences Clus...tion no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99...for each species CRE: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 OTAU: 0 CME: 0 GT

  9. Gclust Server: 147399 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 147399 OSA_Os06g0542000 Cluster Sequences - 144 no annotation 1 1.00e-80 14.29 0.0 ...0.0 0.0 0.0 0.0 Show 147399 Cluster ID 147399 Sequence ID OSA_Os06g0542000 Link to cluster sequences Cluster... Sequences 1 Homologs 1 Clustering threshold 1.00e-80 Plants and algae (7species)...ies not appearing in this cluster ATH: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS: 0 Te

  10. Gclust Server: 41998 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 41998 Rhe_RHE_CH02021 Cluster Sequences Related Sequences(152) 203 hypothetical pro...tein 2 1.00e-90 0.0 0.0 0.0 0.0 6.45 0.0 Show 41998 Cluster ID 41998 Sequence ID Rhe_RHE_CH02021 Link to cluster sequences Clus...entative annotation hypothetical protein Number of Sequences 2 Homologs 2 Cluster... Number of Sequences for each species Rhe: 1 Rle: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR

  11. Gclust Server: 38628 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 38628 PoTR_558313 Cluster Sequences - 205 eugene3.00091573 3 1.00e-40 42.86 0.0 0.0... 0.0 0.0 0.0 Show 38628 Cluster ID 38628 Sequence ID PoTR_558313 Link to cluster sequences Cluster Sequences... Link to related sequences - Sequence length 205 Representative annotation eugene3.00091573 Number of Sequences 3 Homologs 3 Clus...: 1 Species not appearing in this cluster PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS: 0 Ter: 0 An

  12. Gclust Server: 149180 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 149180 Mlo_msr1055 Cluster Sequences - 30 hypothetical protein 1 1.00e-07 0.0 0.0 0....0 0.0 3.23 0.0 Show 149180 Cluster ID 149180 Sequence ID Mlo_msr1055 Link to cluster sequences Cluster Sequ...f Sequences 1 Homologs 1 Clustering threshold 1.00e-07 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  13. Gclust Server: 174287 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 174287 HSA_46409494 Cluster Sequences - 135 NP_997318.1 hypothetical protein LOC400...073 ; no annotation 1 1.00e-70 0.0 0.0 0.0 0.0 0.0 12.5 Show 174287 Cluster ID 174287 Sequence ID HSA_46409494 Link to clus...ter sequences Cluster Sequences Link to related sequences - Sequence length 135 Representativ... Sequences 1 Homologs 1 Clustering threshold 1.00e-70 Plants and algae (7species) (%) 0.0 Other Bikonts (Chr... and fungi) (8species) (%) 12.5 Number of Sequences for each species HSA: 1 Species not appearing in this clus

  14. Gclust Server: 190076 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 190076 OSA_Os03g0745000@0 Cluster Sequences - 52 no annotation 1 1.00e-22 14.29 0.0... 0.0 0.0 0.0 0.0 Show 190076 Cluster ID 190076 Sequence ID OSA_Os03g0745000@0 Link to cluster sequences Clus...of Sequences 1 Homologs 1 Clustering threshold 1.00e-22 Plants and algae (7specie...ecies not appearing in this cluster ATH: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS: 0

  15. Gclust Server: 203183 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 203183 Sep_SE2387 Cluster Sequences - 201 hypothetical protein 1 1.00e-99 0.0 0.0 0....0 0.0 3.23 0.0 Show 203183 Cluster ID 203183 Sequence ID Sep_SE2387 Link to cluster sequences Cluster Seque...f Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  16. Gclust Server: 181209 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 181209 Bma_BMAA0673 Cluster Sequences - 381 hypothetical protein 1 1.00e-99 0.0 0.0... 0.0 0.0 3.23 0.0 Show 181209 Cluster ID 181209 Sequence ID Bma_BMAA0673 Link to cluster sequences Cluster S...er of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7spe...Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR:

  17. Gclust Server: 66364 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 66364 CEL_F02A9.6_17553810 Cluster Sequences Related Sequences(296) 1295 glp-1: abn...ormal Germ Line Proliferation family member (glp-1) 1 1.00e-70 0.0 0.0 0.0 0.0 0.0 12.5 Show 66364 Cluster I...es Related Sequences(296) Sequence length 1295 Representative annotation glp-1: a...bnormal Germ Line Proliferation family member (glp-1) Number of Sequences 1 Homologs 1 Clustering threshold

  18. Gclust Server: 51082 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 51082 CEL_K04C2.6_17554314 Cluster Sequences Related Sequences(3) 174 med-2: Mesoderm and Endoderm Determina...es Related Sequences(3) Sequence length 174 Representative annotation med-2: Mesoderm and Endoderm Determi...nation family member (med-2) Number of Sequences 2 Homologs 2 Clustering threshold ...tion family member (med-2) 2 1.00e-90 0.0 0.0 0.0 0.0 0.0 12.5 Show 51082 Cluster I

  19. Gclust Server: 40322 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 40322 CEL_D1022.6_71984662 Cluster Sequences Related Sequences(288) 425 sro-1: Serp...entine Receptor, class O (opsin) family member (sro-1) 2 1.00e-19 0.0 0.0 0.0 0.0 0.0 25.0 Show 40322 Cluste...ences Related Sequences(288) Sequence length 425 Representative annotation sro-1:... Serpentine Receptor, class O (opsin) family member (sro-1) Number of Sequences 2 Homologs 2 Clustering thre

  20. Gclust Server: 114438 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 114438 CEL_H14A12.4_17553886 Cluster Sequences Related Sequences(46) 252 mls-1: Mesodermal Lineage Specifica...ences Related Sequences(46) Sequence length 252 Representative annotation mls-1: Mesodermal Lineage Specif...ication family member (mls-1) Number of Sequences 1 Homologs 1 Clustering threshold...tion family member (mls-1) 1 1.00e-22 0.0 0.0 0.0 0.0 0.0 12.5 Show 114438 Cluster

  1. Gclust Server: 82285 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 82285 CEL_C39E6.4_25151482 Cluster Sequences Related Sequences(296) 341 mls-2: Mesodermal Lineage Specificat...s Related Sequences(296) Sequence length 341 Representative annotation mls-2: Mesodermal Lineage Specifica...tion family member (mls-2) Number of Sequences 1 Homologs 1 Clustering threshold 1....ion family member (mls-2) 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 82285 Cluster ID

  2. Gclust Server: 117083 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 117083 CEL_W02A11.5_17509469 Cluster Sequences Related Sequences(32) 384 bath-34: B...TB and MATH domain containing family member (bath-34) 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 117083 Cluste...quences Related Sequences(32) Sequence length 384 Representative annotation bath-...34: BTB and MATH domain containing family member (bath-34) Number of Sequences 1 Homologs 1 Clustering thres

  3. Gclust Server: 41845 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 41845 CEL_C07D10.2_17531581 Cluster Sequences Related Sequences(169) 397 bath-44: B...TB and MATH domain containing family member (bath-44) 2 1.00e-31 0.0 0.0 0.0 0.0 0.0 12.5 Show 41845 Cluster...ences Related Sequences(169) Sequence length 397 Representative annotation bath-4...4: BTB and MATH domain containing family member (bath-44) Number of Sequences 2 Homologs 2 Clustering thresh

  4. Gclust Server: 123389 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 123389 CEL_F25H9.4_17560192 Cluster Sequences Related Sequences(15) 370 bath-39: BT...B and MATH domain containing family member (bath-39) 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 123389 Cluster...ences Related Sequences(15) Sequence length 370 Representative annotation bath-39...: BTB and MATH domain containing family member (bath-39) Number of Sequences 1 Homologs 1 Clustering thresho

  5. Gclust Server: 114272 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 114272 CEL_F14D2.1_17533183 Cluster Sequences Related Sequences(45) 299 bath-27: BT...B and MATH domain containing family member (bath-27) 1 1.00e-19 0.0 0.0 0.0 0.0 0.0 12.5 Show 114272 Cluster...ences Related Sequences(45) Sequence length 299 Representative annotation bath-27...: BTB and MATH domain containing family member (bath-27) Number of Sequences 1 Homologs 1 Clustering thresho

  6. Gclust Server: 101362 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 101362 CEL_F52C6.10_17534245 Cluster Sequences Related Sequences(126) 301 bath-7: B...TB and MATH domain containing family member (bath-7) 1 9.98e-01 0.0 0.0 0.0 0.0 0.0 12.5 Show 101362 Cluster...uences Related Sequences(126) Sequence length 301 Representative annotation bath-...7: BTB and MATH domain containing family member (bath-7) Number of Sequences 1 Homologs 1 Clustering thresho

  7. Gclust Server: 105066 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 105066 CEL_F12E12.4_17533141 Cluster Sequences Related Sequences(94) 306 bath-31: B...TB and MATH domain containing family member (bath-31) 1 1.00e-25 0.0 0.0 0.0 0.0 0.0 12.5 Show 105066 Cluste...quences Related Sequences(94) Sequence length 306 Representative annotation bath-...31: BTB and MATH domain containing family member (bath-31) Number of Sequences 1 Homologs 1 Clustering thres

  8. Gclust Server: 23504 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 23504 CEL_F14D2.4_71986475 Cluster Sequences Related Sequences(303) 266 bath-29: BT...B and MATH domain containing family member (bath-29) 4 1.00e-70 0.0 0.0 0.0 0.0 0.0 12.5 Show 23504 Cluster ...ces Related Sequences(303) Sequence length 266 Representative annotation bath-29:... BTB and MATH domain containing family member (bath-29) Number of Sequences 4 Homologs 4 Clustering threshol

  9. Gclust Server: 108728 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 108728 CEL_F14D2.13_71986448 Cluster Sequences Related Sequences(76) 249 bath-28: B...TB and MATH domain containing family member (bath-28) 1 1.00e-14 0.0 0.0 0.0 0.0 0.0 12.5 Show 108728 Cluste...quences Related Sequences(76) Sequence length 249 Representative annotation bath-...28: BTB and MATH domain containing family member (bath-28) Number of Sequences 1 Homologs 1 Clustering thres

  10. Gclust Server: 115432 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 115432 CEL_T07H3.2_17536117 Cluster Sequences Related Sequences(38) 315 bath-46: BT...B and MATH domain containing family member (bath-46) 1 1.00e-10 0.0 0.0 0.0 0.0 0.0 12.5 Show 115432 Cluster...ences Related Sequences(38) Sequence length 315 Representative annotation bath-46...: BTB and MATH domain containing family member (bath-46) Number of Sequences 1 Homologs 1 Clustering thresho

  11. Gclust Server: 111105 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 111105 CEL_Y49F6C.5_17537313 Cluster Sequences Related Sequences(61) 243 bath-23: B...TB and MATH domain containing family member (bath-23) 1 1.00e-31 0.0 0.0 0.0 0.0 0.0 12.5 Show 111105 Cluste...quences Related Sequences(61) Sequence length 243 Representative annotation bath-...23: BTB and MATH domain containing family member (bath-23) Number of Sequences 1 Homologs 1 Clustering thres

  12. Gclust Server: 108391 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 108391 CEL_B0047.3_17531219 Cluster Sequences Related Sequences(77) 242 bath-24: BT...B and MATH domain containing family member (bath-24) 1 1.00e-28 0.0 0.0 0.0 0.0 0.0 12.5 Show 108391 Cluster...ences Related Sequences(77) Sequence length 242 Representative annotation bath-24...: BTB and MATH domain containing family member (bath-24) Number of Sequences 1 Homologs 1 Clustering thresho

  13. Gclust Server: 197368 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 197368 Bja_bsr4406 Cluster Sequences - 65 hypothetical protein 1 1.00e-28 0.0 0.0 0....0 0.0 3.23 0.0 Show 197368 Cluster ID 197368 Sequence ID Bja_bsr4406 Link to cluster sequences Cluster Sequ...f Sequences 1 Homologs 1 Clustering threshold 1.00e-28 Plants and algae (7species...ies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TP

  14. Gclust Server: 119249 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 119249 PTR_8293 Cluster Sequences Related Sequences(25) 67 gw1.5.385.1 1 1.00e-31 0....0 11.11 0.0 0.0 0.0 0.0 Show 119249 Cluster ID 119249 Sequence ID PTR_8293 Link to cluster sequences Cluste....5.385.1 Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-31 Plants an...pecies PTR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH:

  15. Gclust Server: 194925 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 194925 PPT_99446 Cluster Sequences - 160 fgenesh1_pg.scaffold_391000010; no annotat...ion 1 1.00e-80 14.29 0.0 0.0 0.0 0.0 0.0 Show 194925 Cluster ID 194925 Sequence ID PPT_99446 Link to cluster sequences Clus...sh1_pg.scaffold_391000010; no annotation Number of Sequences 1 Homologs 1 Cluster...0 Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CR

  16. Gclust Server: 30669 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 30669 DPTM_GSPATP00006398001 Cluster Sequences Related Sequences(85) 278 no annotat...ion 3 1.00e-70 0.0 11.11 0.0 0.0 0.0 0.0 Show 30669 Cluster ID 30669 Sequence ID DPTM_GSPATP00006398001 Link to clus...Representative annotation no annotation Number of Sequences 3 Homologs 3 Clusteri... Number of Sequences for each species DPTM: 3 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PP

  17. Gclust Server: 197245 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 197245 PPT_78285 Cluster Sequences - 472 fgenesh1_pg.scaffold_70000102; no annotati...on 1 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 197245 Cluster ID 197245 Sequence ID PPT_78285 Link to cluster sequences Clus...h1_pg.scaffold_70000102; no annotation Number of Sequences 1 Homologs 1 Clusterin...Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE:

  18. Gclust Server: 43399 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 43399 PoTR_219482 Cluster Sequences Related Sequences(72) 252 gw1.VII.3787.1 2 1.00...e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 43399 Cluster ID 43399 Sequence ID PoTR_219482 Link to cluster sequences Clus...tion gw1.VII.3787.1 Number of Sequences 2 Homologs 2 Clustering threshold 1.00e-9... for each species PoTR: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 G

  19. Gclust Server: 125015 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 125015 PFA_PFF0925w Cluster Sequences Related Sequences(12) 380 hypothetical protei...n 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 125015 Cluster ID 125015 Sequence ID PFA_PFF0925w Link to cluster sequences Clus...tive annotation hypothetical protein Number of Sequences 1 Homologs 1 Clustering ...mber of Sequences for each species PFA: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0

  20. Gclust Server: 3010 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 3010 DCGR_CAGL0L09801g Cluster Sequences Related Sequences(31) 319 - 32 1.00e-28 10...0.0 77.78 0.0 0.0 0.0 100.0 Show 3010 Cluster ID 3010 Sequence ID DCGR_CAGL0L09801g Link to cluster sequences Clus...ation - Number of Sequences 32 Homologs 32 Clustering threshold 1.00e-28 Plants a...CGR: 2 DKLA: 2 NCR: 2 DPTM: 1 TET: 1 NGR: 1 HSA: 2 DME: 1 CEL: 1 Species not appearing in this cluster GTH:

  1. Gclust Server: 48684 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 48684 PoTR_763349 Cluster Sequences Related Sequences(6) 125 fgenesh4_pg.C_LG_VI001...659 2 1.00e-16 28.57 0.0 0.0 0.0 0.0 0.0 Show 48684 Cluster ID 48684 Sequence ID PoTR_763349 Link to cluster sequences Clus...ve annotation fgenesh4_pg.C_LG_VI001659 Number of Sequences 2 Homologs 2 Clusteri... Number of Sequences for each species OSA: 1 PoTR: 1 Species not appearing in this cluster ATH: 0 PPT: 0 CRE

  2. Gclust Server: 166605 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 166605 Pm7_P9303_19711 Cluster Sequences - 93 hypothetical protein 1 1.00e-45 0.0 0....0 4.0 0.0 0.0 0.0 Show 166605 Cluster ID 166605 Sequence ID Pm7_P9303_19711 Link to cluster sequences Clust...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-45 Plants and algae (7...1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR

  3. Gclust Server: 27720 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 27720 Npun1_NpF3923 Cluster Sequences - 65 unknown protein [Nostoc sp. PCC 7120] 4 ...1.00e-22 0.0 0.0 16.0 0.0 0.0 0.0 Show 27720 Cluster ID 27720 Sequence ID Npun1_NpF3923 Link to cluster sequences Clus...tein [Nostoc sp. PCC 7120] Number of Sequences 4 Homologs 4 Clustering threshold ...uences for each species Ter: 1 Ana: 1 Ava: 1 Npun: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoT

  4. Gclust Server: 1287 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 1287 PPT_90222 Cluster Sequences Related Sequences(23) 210 fgenesh1_pg.scaffold_194...000057; no annotation 63 1.00e-19 85.71 77.78 0.0 0.0 3.23 87.5 Show 1287 Cluster ID 1287 Sequence ID PPT_90222 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(23) Sequence len...umber of Sequences 63 Homologs 63 Clustering threshold 1.00e-19 Plants and algae (7species) (%) 85.71 Other ... NGR: 2 HSA: 7 CEL: 5 Species not appearing in this cluster CME: 0 GTH: 0 PFA: 0

  5. Gclust Server: 158945 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 158945 CEL_T07D1.3_17569659 Cluster Sequences - 144 T07D1.3 1 1.00e-80 0.0 0.0 0.0 ...0.0 0.0 12.5 Show 158945 Cluster ID 158945 Sequence ID CEL_T07D1.3_17569659 Link to cluster sequences Cluste...r Sequences Link to related sequences - Sequence length 144 Representative annotation T07D1.3 Number of Sequences 1 Homologs 1 Clus...fungi) (8species) (%) 12.5 Number of Sequences for each species CEL: 1 Species not appearing in this clus

  6. Gclust Server: 192978 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 192978 DPTM_GSPATP00022593001 Cluster Sequences - 224 no annotation 1 1.00e-99 0.0 ...11.11 0.0 0.0 0.0 0.0 Show 192978 Cluster ID 192978 Sequence ID DPTM_GSPATP00022593001 Link to cluster sequences Clus...on Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and alga... DPTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA

  7. Gclust Server: 50654 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 50654 DPTM_GSPATP00037896001 Cluster Sequences Related Sequences(3) 438 no annotati...on 2 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 50654 Cluster ID 50654 Sequence ID DPTM_GSPATP00037896001 Link to clus...presentative annotation no annotation Number of Sequences 2 Homologs 2 Clustering...umber of Sequences for each species DPTM: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT:

  8. Gclust Server: 141343 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 141343 Mes_Meso_2172 Cluster Sequences - 128 hypothetical protein 1 1.00e-60 0.0 0....0 0.0 0.0 3.23 0.0 Show 141343 Cluster ID 141343 Sequence ID Mes_Meso_2172 Link to cluster sequences Cluster...mber of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and algae (7s...1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR

  9. Gclust Server: 176794 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 176794 NGR_80044 Cluster Sequences - 185 estExt_fgeneshNG_pg.C_290066; no annotatio...n 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 176794 Cluster ID 176794 Sequence ID NGR_80044 Link to cluster sequences Clus...fgeneshNG_pg.C_290066; no annotation Number of Sequences 1 Homologs 1 Clustering ...mber of Sequences for each species NGR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0

  10. Gclust Server: 153818 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 153818 Pst_PSPTO_3417 Cluster Sequences - 119 hypothetical protein 1 1.00e-60 0.0 0....0 0.0 0.0 3.23 0.0 Show 153818 Cluster ID 153818 Sequence ID Pst_PSPTO_3417 Link to cluster sequences Clust...Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and algae (...: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 P

  11. Gclust Server: 106717 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 106717 Hal_VNG1992G=pgi Cluster Sequences Related Sequences(94) 426 Pgi 1 1.00e-25 ...0.0 0.0 0.0 0.0 3.23 0.0 Show 106717 Cluster ID 106717 Sequence ID Hal_VNG1992G=pgi Link to cluster sequences Clus...ation Pgi Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-25 Plants a...pecies Hal: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH:

  12. Gclust Server: 205065 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 205065 PPT_66926 Cluster Sequences - 334 fgenesh1_pg.scaffold_12000211; no annotati...on 1 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 205065 Cluster ID 205065 Sequence ID PPT_66926 Link to cluster sequences Clus...h1_pg.scaffold_12000211; no annotation Number of Sequences 1 Homologs 1 Clusterin...Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE:

  13. Gclust Server: 55606 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 55606 PHRA_74553 Cluster Sequences - 475 fgenesh1_pg.C_scaffold_8000154; no annotat...ion 2 1.00e-99 0.0 22.22 0.0 0.0 0.0 0.0 Show 55606 Cluster ID 55606 Sequence ID PHRA_74553 Link to cluster sequences Clus...h1_pg.C_scaffold_8000154; no annotation Number of Sequences 2 Homologs 2 Clusteri... Number of Sequences for each species PHRA: 1 PHSO: 1 Species not appearing in this cluster ATH: 0 OSA: 0 Po

  14. Gclust Server: 146014 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 146014 OSA_@632 Cluster Sequences - 273 no annotation 1 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 146014 Clus...ter ID 146014 Sequence ID OSA_@632 Link to cluster sequences Cluster Sequences Link ...to related sequences - Sequence length 273 Representative annotation no annotation Number of Sequences 1 Homologs 1 Clus...species) (%) 0.0 Number of Sequences for each species OSA: 1 Species not appearing in this clus

  15. Gclust Server: 6169 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 6169 PPT_118352 Cluster Sequences Related Sequences(343) 307 e_gw1.24.3.1; no annot...ation 17 1.00e-60 42.86 66.67 0.0 0.0 0.0 12.5 Show 6169 Cluster ID 6169 Sequence ID PPT_118352 Link to cluster sequences Clus...ntative annotation e_gw1.24.3.1; no annotation Number of Sequences 17 Homologs 17 Clus...2 NGR: 1 HSA: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 Ter:

  16. Gclust Server: 111630 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 111630 Mac_MA3436 Cluster Sequences Related Sequences(60) 316 hypothetical protein ...1 1.00e-99 0.0 0.0 0.0 0.0 3.23 0.0 Show 111630 Cluster ID 111630 Sequence ID Mac_MA3436 Link to cluster sequences Clus...annotation hypothetical protein Number of Sequences 1 Homologs 1 Clustering thres...f Sequences for each species Mac: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE:

  17. Gclust Server: 22312 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 22312 Ava_Ava_4112 Cluster Sequences - 78 hypothetical protein 5 1.00e-22 0.0 0.0 1...2.0 0.0 0.0 0.0 Show 22312 Cluster ID 22312 Sequence ID Ava_Ava_4112 Link to cluster sequences Cluster Seque... Sequences 5 Homologs 5 Clustering threshold 1.00e-22 Plants and algae (7species)...3 Npun: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PF

  18. Gclust Server: 21508 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 21508 Pst_PSPTO_0716 Cluster Sequences Related Sequences(1) 90 DNA-binding protein ...5 1.00e-14 0.0 0.0 0.0 0.0 6.45 0.0 Show 21508 Cluster ID 21508 Sequence ID Pst_PSPTO_0716 Link to cluster sequences Clus...annotation DNA-binding protein Number of Sequences 5 Homologs 5 Clustering thresh... Sequences for each species Pst: 4 Rso: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0

  19. Gclust Server: 143167 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 143167 Ccr_CC_2621 Cluster Sequences - 145 hypothetical protein 1 1.00e-70 0.0 0.0 ...0.0 0.0 3.23 0.0 Show 143167 Cluster ID 143167 Sequence ID Ccr_CC_2621 Link to cluster sequences Cluster Seq... of Sequences 1 Homologs 1 Clustering threshold 1.00e-70 Plants and algae (7speci...ecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  20. Gclust Server: 203799 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 203799 CRE_141529 Cluster Sequences - 3198 no annotation 1 1.00e+00 14.29 0.0 0.0 0....0 0.0 0.0 Show 203799 Cluster ID 203799 Sequence ID CRE_141529 Link to cluster sequences Cluster Sequences ...Link to related sequences - Sequence length 3198 Representative annotation no annotation Number of Sequences 1 Homologs 1 Clus...gi) (8species) (%) 0.0 Number of Sequences for each species CRE: 1 Species not appearing in this clus

  1. Gclust Server: 158019 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 158019 TET_20.m00426 Cluster Sequences - 202 hypothetical protein chr_0_8254373_20;... no annotation 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 158019 Cluster ID 158019 Sequence ID TET_20.m00426 Link to clus...ter sequences Cluster Sequences Link to related sequences - Sequence length 202 Representative a...nnotation hypothetical protein chr_0_8254373_20; no annotation Number of Sequences 1 Homologs 1 Clus...ngi) (8species) (%) 0.0 Number of Sequences for each species TET: 1 Species not appearing in this cluster AT

  2. Gclust Server: 143000 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 143000 TET_72.m00153 Cluster Sequences - 192 hypothetical protein chr_0_8254786_72;... no annotation 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 143000 Cluster ID 143000 Sequence ID TET_72.m00153 Link to clus...ter sequences Cluster Sequences Link to related sequences - Sequence length 192 Representative a...nnotation hypothetical protein chr_0_8254786_72; no annotation Number of Sequences 1 Homologs 1 Clus...ngi) (8species) (%) 0.0 Number of Sequences for each species TET: 1 Species not appearing in this cluster AT

  3. Gclust Server: 31842 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 31842 OTAU_9239 Cluster Sequences Related Sequences(56) 483 fgenesh1_pg.C_Chr_01.00...01000005 3 1.00e-25 28.57 11.11 0.0 0.0 0.0 0.0 Show 31842 Cluster ID 31842 Sequence ID OTAU_9239 Link to cluster sequences Clus...entative annotation fgenesh1_pg.C_Chr_01.0001000005 Number of Sequences 3 Homologs 3 Clus...ecies) (%) 0.0 Number of Sequences for each species OTAU: 1 CME: 1 TPS: 1 Species not appearing in this clus

  4. Gclust Server: 186247 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 186247 PPT_81297 Cluster Sequences - 173 fgenesh1_pg.scaffold_93000099; no annotati...on 1 1.00e-90 14.29 0.0 0.0 0.0 0.0 0.0 Show 186247 Cluster ID 186247 Sequence ID PPT_81297 Link to cluster sequences Clus...h1_pg.scaffold_93000099; no annotation Number of Sequences 1 Homologs 1 Clusterin...Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE:

  5. Gclust Server: 82314 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 82314 Atu_Atu4157=putA Cluster Sequences Related Sequences(293) 1228 proline dehydr...ogenase 1 1.00e-99 0.0 0.0 0.0 0.0 3.23 0.0 Show 82314 Cluster ID 82314 Sequence ID Atu_Atu4157=putA Link to cluster sequences Clus...epresentative annotation proline dehydrogenase Number of Sequences 1 Homologs 1 Clus...%) 0.0 Number of Sequences for each species Atu: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR:

  6. Gclust Server: 7320 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 7320 Syn_slr0746=stpA Cluster Sequences - 422 glucosylglycerolphosphate phosphatase... 15 1.00e-70 0.0 0.0 60.0 0.0 0.0 0.0 Show 7320 Cluster ID 7320 Sequence ID Syn_slr0746=stpA Link to cluster sequences Clus...sylglycerolphosphate phosphatase Number of Sequences 15 Homologs 15 Clustering th... Pm7: 1 Pm8: 1 Pm9: 1 PmA: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU:

  7. Gclust Server: 140201 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 140201 DPTM_GSPATP00017218001 Cluster Sequences - 193 no annotation 1 1.00e-99 0.0 ...11.11 0.0 0.0 0.0 0.0 Show 140201 Cluster ID 140201 Sequence ID DPTM_GSPATP00017218001 Link to cluster sequences Clus...on Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and alga... DPTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA

  8. Gclust Server: 19257 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 19257 PHRA_93453 Cluster Sequences Related Sequences(411) 450 C_scaffold_2000055; n...o annotation 5 1.00e-08 0.0 22.22 4.0 0.0 0.0 12.5 Show 19257 Cluster ID 19257 Sequence ID PHRA_93453 Link to cluster sequences Clus...epresentative annotation C_scaffold_2000055; no annotation Number of Sequences 5 Homologs 5 Clus... (8species) (%) 12.5 Number of Sequences for each species Pm2: 1 PHRA: 1 PHSO: 2 HSA: 1 Species not appearing in this clus

  9. Gclust Server: 64943 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 64943 PPT_94164 Cluster Sequences - 1025 fgenesh1_pg.scaffold_256000005; no annotat...ion 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 64943 Cluster ID 64943 Sequence ID PPT_94164 Link to cluster sequences Clus...h1_pg.scaffold_256000005; no annotation Number of Sequences 1 Homologs 1 Clusteri... Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE

  10. Gclust Server: 204002 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 204002 Atu_Atu2317 Cluster Sequences - 198 hypothetical protein 1 1.00e-99 0.0 0.0 ...0.0 0.0 3.23 0.0 Show 204002 Cluster ID 204002 Sequence ID Atu_Atu2317 Link to cluster sequences Cluster Seq... of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7speci...ecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  11. Gclust Server: 183918 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 183918 DME_CG30197_24653660 Cluster Sequences - 113 CG30197: CG30197-PA 1 1.00e-60 ...0.0 0.0 0.0 0.0 0.0 12.5 Show 183918 Cluster ID 183918 Sequence ID DME_CG30197_24653660 Link to cluster sequences Clus...G30197-PA Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants a...pecies DME: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH:

  12. Gclust Server: 162180 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 162180 Mac_MA1039 Cluster Sequences - 79 hypothetical protein 1 1.00e-35 0.0 0.0 0....0 0.0 3.23 0.0 Show 162180 Cluster ID 162180 Sequence ID Mac_MA1039 Link to cluster sequences Cluster Sequen...Sequences 1 Homologs 1 Clustering threshold 1.00e-35 Plants and algae (7species) ...s not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS:

  13. Gclust Server: 197447 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 197447 PPT_64221 Cluster Sequences - 129 fgenesh1_pg.scaffold_2000098; no annotatio...n 1 1.00e-70 14.29 0.0 0.0 0.0 0.0 0.0 Show 197447 Cluster ID 197447 Sequence ID PPT_64221 Link to cluster sequences Clus...1_pg.scaffold_2000098; no annotation Number of Sequences 1 Homologs 1 Clustering ...mber of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE: 0

  14. Gclust Server: 34373 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 34373 PTR_42876 Cluster Sequences - 1545 estExt_fgenesh1_pg.C_chr_10574 3 1.00e-99 ...0.0 22.22 0.0 0.0 0.0 0.0 Show 34373 Cluster ID 34373 Sequence ID PTR_42876 Link to cluster sequences Cluste...chr_10574 Number of Sequences 3 Homologs 3 Clustering threshold 1.00e-99 Plants a...species PTR: 1 TPS: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME:

  15. Gclust Server: 17219 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 17219 DPTM_GSPATP00004243001 Cluster Sequences Related Sequences(15) 337 no annotat...ion 6 1.00e-50 0.0 11.11 0.0 0.0 0.0 0.0 Show 17219 Cluster ID 17219 Sequence ID DPTM_GSPATP00004243001 Link to clus...Representative annotation no annotation Number of Sequences 6 Homologs 6 Clusteri... Number of Sequences for each species DPTM: 6 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PP

  16. Gclust Server: 59871 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 59871 NpunA_pNPAR295 Cluster Sequences - 80 - 2 1.00e-35 0.0 0.0 4.0 0.0 0.0 0.0 Show 59871 Clus...ter ID 59871 Sequence ID NpunA_pNPAR295 Link to cluster sequences Cluster Sequences Link to rel...ated sequences - Sequence length 80 Representative annotation - Number of Sequences 2 Homologs 2 Clustering ...er of Sequences for each species Npun: 2 Species not appearing in this cluster AT

  17. Gclust Server: 96142 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 96142 Glv_gvip218=narB Cluster Sequences Related Sequences(208) 692 nitrate reducta...se 1 1.00e-35 0.0 0.0 4.0 0.0 0.0 0.0 Show 96142 Cluster ID 96142 Sequence ID Glv_gvip218=narB Link to cluster sequences Clus...tative annotation nitrate reductase Number of Sequences 1 Homologs 1 Clustering t...r of Sequences for each species Glv: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CR

  18. Gclust Server: 181097 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 181097 PoTR_772628 Cluster Sequences - 122 fgenesh4_pg.C_LG_XII000403 1 1.00e-60 14....29 0.0 0.0 0.0 0.0 0.0 Show 181097 Cluster ID 181097 Sequence ID PoTR_772628 Link to cluster sequences Clus...000403 Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and ...cies PoTR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0

  19. Gclust Server: 88987 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 88987 NGR_77826 Cluster Sequences - 1422 estExt_fgeneshNG_pg.C_10517; no annotation... 1 1.00e+00 0.0 11.11 0.0 0.0 0.0 0.0 Show 88987 Cluster ID 88987 Sequence ID NGR_77826 Link to cluster sequences Clus...eneshNG_pg.C_10517; no annotation Number of Sequences 1 Homologs 1 Clustering thr...r of Sequences for each species NGR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CR

  20. Gclust Server: 136518 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 136518 Pst_PSPTO_1388=hrpG Cluster Sequences - 143 type III secretion protein HrpG ...1 1.00e-70 0.0 0.0 0.0 0.0 3.23 0.0 Show 136518 Cluster ID 136518 Sequence ID Pst_PSPTO_1388=hrpG Link to cluster sequences Clus...type III secretion protein HrpG Number of Sequences 1 Homologs 1 Clustering thres...f Sequences for each species Pst: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE:

  1. Gclust Server: 142841 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 142841 Npun1_NpF0960 Cluster Sequences - 75 - 1 1.00e-35 0.0 0.0 4.0 0.0 0.0 0.0 Show 142841 Clus...ter ID 142841 Sequence ID Npun1_NpF0960 Link to cluster sequences Cluster Sequences Link to re...lated sequences - Sequence length 75 Representative annotation - Number of Sequences 1 Homologs 1 Clustering...ber of Sequences for each species Npun: 1 Species not appearing in this cluster A

  2. Gclust Server: 193537 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 193537 DPTM_GSPATP00039568001 Cluster Sequences - 33 no annotation 1 1.00e-10 0.0 1...1.11 0.0 0.0 0.0 0.0 Show 193537 Cluster ID 193537 Sequence ID DPTM_GSPATP00039568001 Link to cluster sequences Clus... Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-10 Plants and algae ...PTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA:

  3. Gclust Server: 200684 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 200684 DME_CG15234_21358285 Cluster Sequences - 75 CG15234: CG15234-PA 1 1.00e-35 0....0 0.0 0.0 0.0 0.0 12.5 Show 200684 Cluster ID 200684 Sequence ID DME_CG15234_21358285 Link to cluster sequences Clus...5234-PA Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-35 Plants and...cies DME: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0

  4. Gclust Server: 166315 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 166315 Bsu_BSU11080=yitQ Cluster Sequences - 245 hypothetical protein 1 1.00e-99 0....0 0.0 0.0 0.0 3.23 0.0 Show 166315 Cluster ID 166315 Sequence ID Bsu_BSU11080=yitQ Link to cluster sequences Clus...otein Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and a...es Bsu: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PF

  5. Gclust Server: 42981 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 42981 DPTM_GSPATP00029415001 Cluster Sequences Related Sequences(56) 153 no annotat...ion 2 1.00e-90 0.0 11.11 0.0 0.0 0.0 0.0 Show 42981 Cluster ID 42981 Sequence ID DPTM_GSPATP00029415001 Link to clus...Representative annotation no annotation Number of Sequences 2 Homologs 2 Clusteri... Number of Sequences for each species DPTM: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PP

  6. Gclust Server: 172932 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 172932 NGR_78062 Cluster Sequences - 230 estExt_fgeneshNG_pg.C_30248; no annotation... 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 172932 Cluster ID 172932 Sequence ID NGR_78062 Link to cluster sequences Clus...geneshNG_pg.C_30248; no annotation Number of Sequences 1 Homologs 1 Clustering th...er of Sequences for each species NGR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 C

  7. Gclust Server: 154846 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 154846 Hal_VNG0357H Cluster Sequences - 142 hypothetical protein 1 1.00e-70 0.0 0.0... 0.0 0.0 3.23 0.0 Show 154846 Cluster ID 154846 Sequence ID Hal_VNG0357H Link to cluster sequences Cluster S...er of Sequences 1 Homologs 1 Clustering threshold 1.00e-70 Plants and algae (7spe...Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR:

  8. Gclust Server: 128586 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 128586 Sme_SMa1878 Cluster Sequences Related Sequences(7) 51 Putative transposase 1... 1.00e-22 0.0 0.0 0.0 0.0 3.23 0.0 Show 128586 Cluster ID 128586 Sequence ID Sme_SMa1878 Link to cluster sequences Clus...notation Putative transposase Number of Sequences 1 Homologs 1 Clustering thresho...Sequences for each species Sme: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0

  9. Gclust Server: 71170 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 71170 DPTM_GSPATP00026607001 Cluster Sequences Related Sequences(468) 552 no annota...tion 1 9.98e-01 0.0 11.11 0.0 0.0 0.0 0.0 Show 71170 Cluster ID 71170 Sequence ID DPTM_GSPATP00026607001 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(468) Sequence length 55...2 Representative annotation no annotation Number of Sequences 1 Homologs 1 Cluste....0 Number of Sequences for each species DPTM: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0

  10. Gclust Server: 182942 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 182942 GTHnm1_orf122 Cluster Sequences - 122 hypothetical protein 1 1.00e-60 0.0 11....11 0.0 0.0 0.0 0.0 Show 182942 Cluster ID 182942 Sequence ID GTHnm1_orf122 Link to cluster sequences Cluste...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and algae (7...: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 PFA: 0 PTR: 0 T

  11. Gclust Server: 156437 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 156437 TET_92.m00104 Cluster Sequences - 73 hypothetical protein chr_0_8254653_92; ...no annotation 1 1.00e-31 0.0 11.11 0.0 0.0 0.0 0.0 Show 156437 Cluster ID 156437 Sequence ID TET_92.m00104 Link to clus...ter sequences Cluster Sequences Link to related sequences - Sequence length 73 Representative ann...otation hypothetical protein chr_0_8254653_92; no annotation Number of Sequences 1 Homologs 1 Clus...i) (8species) (%) 0.0 Number of Sequences for each species TET: 1 Species not appearing in this cluster ATH:

  12. Gclust Server: 198361 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 198361 Bja_blr0164 Cluster Sequences - 105 hypothetical protein 1 1.00e-50 0.0 0.0 ...0.0 0.0 3.23 0.0 Show 198361 Cluster ID 198361 Sequence ID Bja_blr0164 Link to cluster sequences Cluster Seq... of Sequences 1 Homologs 1 Clustering threshold 1.00e-50 Plants and algae (7speci...ecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  13. Gclust Server: 182407 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 182407 CRE_194153 Cluster Sequences - 312 no annotation 1 1.00e-99 14.29 0.0 0.0 0....0 0.0 0.0 Show 182407 Cluster ID 182407 Sequence ID CRE_194153 Link to cluster sequences Cluster Sequences L...ink to related sequences - Sequence length 312 Representative annotation no annotation Number of Sequences 1 Homologs 1 Clus...) (8species) (%) 0.0 Number of Sequences for each species CRE: 1 Species not appearing in this clus

  14. Gclust Server: 119995 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 119995 CRE_149042 Cluster Sequences Related Sequences(23) 278 no annotation 1 1.00e...-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 119995 Cluster ID 119995 Sequence ID CRE_149042 Link to cluster sequences Clus...tion no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99...for each species CRE: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 OTAU: 0 CME: 0 GT

  15. Gclust Server: 185297 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 185297 PPT_74211 Cluster Sequences - 171 fgenesh1_pg.scaffold_46000053; no annotati...on 1 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 185297 Cluster ID 185297 Sequence ID PPT_74211 Link to cluster sequences Clus...h1_pg.scaffold_46000053; no annotation Number of Sequences 1 Homologs 1 Clusterin...Number of Sequences for each species PPT: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CRE:

  16. Gclust Server: 44673 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 44673 CEL_K10D11.3_32566031 Cluster Sequences Related Sequences(36) 460 K10D11.3 2 ...1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 44673 Cluster ID 44673 Sequence ID CEL_K10D11.3_32566031 Link to cluster sequences Clus...tative annotation K10D11.3 Number of Sequences 2 Homologs 2 Clustering threshold ...uences for each species CEL: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTA

  17. Gclust Server: 93800 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 93800 Ava_Ava_0183 Cluster Sequences - 400 Peptidase M23B 1 1.00e+00 0.0 0.0 4.0 0....0 0.0 0.0 Show 93800 Cluster ID 93800 Sequence ID Ava_Ava_0183 Link to cluster sequences Cluster Sequences L...ink to related sequences - Sequence length 400 Representative annotation Peptidase M23B Number of Sequences 1 Homologs 1 Clus... (8species) (%) 0.0 Number of Sequences for each species Ava: 1 Species not appearing in this clus

  18. Gclust Server: 113603 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 113603 CRE_124110 Cluster Sequences Related Sequences(22) 121 no annotation 1 1.00e...-70 14.29 0.0 0.0 0.0 0.0 0.0 Show 113603 Cluster ID 113603 Sequence ID CRE_124110 Link to cluster sequences Clus...tion no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-70...for each species CRE: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 OTAU: 0 CME: 0 GT

  19. Gclust Server: 168744 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 168744 Pm7_P9303_13681 Cluster Sequences - 63 hypothetical protein 1 1.00e-31 0.0 0....0 4.0 0.0 0.0 0.0 Show 168744 Cluster ID 168744 Sequence ID Pm7_P9303_13681 Link to cluster sequences Clust...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-31 Plants and algae (7...1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR

  20. Gclust Server: 63265 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 63265 PoTR_573697 Cluster Sequences - 110 eugene3.00190171 2 1.00e-31 14.29 0.0 0.0... 0.0 0.0 0.0 Show 63265 Cluster ID 63265 Sequence ID PoTR_573697 Link to cluster sequences Cluster Sequences... Link to related sequences - Sequence length 110 Representative annotation eugene3.00190171 Number of Sequences 2 Homologs 2 Clus...fungi) (8species) (%) 0.0 Number of Sequences for each species PoTR: 2 Species not appearing in this clus

  1. Gclust Server: 44910 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 44910 TPS_4756 Cluster Sequences Related Sequences(57) 626 fgenesh1_pg.C_chr_400070...6 2 1.00e-45 0.0 22.22 0.0 0.0 0.0 0.0 Show 44910 Cluster ID 44910 Sequence ID TPS_4756 Link to cluster sequences Clus...nnotation fgenesh1_pg.C_chr_4000706 Number of Sequences 2 Homologs 2 Clustering t...ber of Sequences for each species PTR: 1 TPS: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0

  2. Structure solution with ARCIMBOLDO using fragments derived from distant homology models.

    Science.gov (United States)

    Sammito, Massimo; Meindl, Kathrin; de Ilarduya, Iñaki M; Millán, Claudia; Artola-Recolons, Cecilia; Hermoso, Juan A; Usón, Isabel

    2014-09-01

    Molecular replacement, one of the general methods used to solve the crystallographic phase problem, relies on the availability of suitable models for placement in the unit cell of the unknown structure in order to provide initial phases. ARCIMBOLDO, originally conceived for ab initio phasing, operates at the limit of this approach, using small, very accurate fragments such as polyalanine α-helices. A distant homolog may contain accurate building blocks, but it may not be evident which sub-structure is the most suitable purely from the degree of conservation. Trying out all alternative possibilities in a systematic way is computationally expensive, even if effective. In the present study, the solution of the previously unknown structure of MltE, an outer membrane-anchored endolytic peptidoglycan lytic transglycosylase from Escherichia coli, is described. The asymmetric unit contains a dimer of this 194 amino acid protein. The closest available homolog was the catalytic domain of Slt70 (PDB code 1QTE). Originally, this template was used omitting contiguous spans of aminoacids and setting as many ARCIMBOLDO runs as models, each aiming to locate two copies sequentially with PHASER. Fragment trimming against the correlation coefficient prior to expansion through density modification and autotracing in SHELXE was essential. Analysis of the figures of merit led to the strategy to optimize the search model against the experimental data now implemented within ARCIMBOLDO-SHREDDER (http://chango.ibmb.csic.es/SHREDDER). In this strategy, the initial template is systematically shredded, and fragments are scored against each unique solution of the rotation function. Results are combined into a score per residue and the template is trimmed accordingly.

  3. Theoretical model of the three-dimensional structure of a disease resistance gene homolog encoding resistance protein in Vigna mungo.

    Science.gov (United States)

    Basak, Jolly; Bahadur, Ranjit P

    2006-10-01

    Plant disease resistance (R) genes, the key players of innate immunity system in plants encode 'R' proteins. 'R' protein recognizes product of avirulance gene from the pathogen and activate downstream signaling responses leading to disease resistance. No three dimensional (3D) structural information of any 'R' proteins is available as yet. We have reported a 'R' gene homolog, the 'VMYR1', encoding 'R' protein in Vigna mungo. Here, we describe the homology modeling of the 'VMYR1' protein. The model was created by using the 3D structure of an ATP-binding cassette transporter protein from Vibrio cholerae as a template. The strategy for homology modeling was based on the high structural conservation in the superfamily of P-loop containing nucleoside triphosphate hydrolase in which target and template proteins belong. This is the first report of theoretical model structure of any 'R' proteins.

  4. 3D structure prediction of lignolytic enzymes lignin peroxidase and manganese peroxidase based on homology modelling

    Directory of Open Access Journals (Sweden)

    SWAPNIL K. KALE

    2016-04-01

    Full Text Available Lignolytic enzymes have great biotechnological value in biopulping, biobleaching, and bioremediation. Manganese peroxidase (EC 1:11:1:13 and lignin peroxidase (EC 1:11:1:14 are extracellular and hem-containing peroxidases that catalyze H2O2-dependent oxidation of lignin. Because of their ability to catalyse oxidation of a wide range of organic compounds and even some inorganic compounds, they got tremendous industrial importance. In this study, 3D structure of lignin and manganese peroxidase has been predicted on the basis of homology modeling using Swiss PDB workspace. The physicochemical properties like molecular weight, isoelectric point, Grand average of hydropathy, instability and aliphatic index of the target enzymes were performed using Protparam. The predicted secondary structure of MnP has 18 helices and 6 strands, while LiP has 20 helices and 4 strands. Generated 3D structure was visualized in Pymol. The generated model for MnP and LiP has Z-score Qmean of 0.01 and -0.71, respectively. The predicted models were validated through Ramachandran Plot, which indicated that 96.1 and 95.5% of the residues are in most favored regions for MnP and LiP respectively. The quality of predicted models were assessed and confirmed by VERIFY 3D, PROCHECK and ERRAT. The modeled structure of MnP and LiP were submitted to the Protein Model Database.

  5. Secondary structure and 3D homology modeling of swine leukocyte antigen class 2 (SLA-2) molecules.

    Science.gov (United States)

    Gao, Feng-Shan; Xu, Chong-bo; Long, Yi-hou; Xia, Chun

    2009-01-01

    No information to date is available to elucidate the structure of swine leukocyte antigen class I (SLA-I) molecule which is comprised by a heavy chain of SLA-I non-covalently associated with a light chain, beta(2)-microglobulin (beta(2)m) proteins. Presently, one of SLA-I gene SLA-2 and beta(2)m gene were expressed as soluble maltose binding proteins (MBP-proteins) in a pMAL-p2X/Escherichia coli TB1 system and identified by western blotting with anti-MBP polyclonal antibodies. The expressed proteins MBP-SLA-2 and MBP-beta(2)m were purified on amylose affinity columns followed by DEAE-Sepharose. The purified products were cleaved by Factor Xa, respectively, and the interest of proteins SLA-2 and beta(2)m were purified on amylose affinity columns followed by separation from MBP on DEAE-Sepharose. The secondary structures of SLA-2 and beta(2)m were analyzed by circular dichroism (CD) spectrophotometry. The three-dimensional (3D) structure of their peptide-binding domain (PBD) was modeled-based sequence homology. The content of the alpha-helix, beta-sheet, turn, and random coil in the SLA-2 protein were 76, 95, 36, and 67aa, respectively. In the 98aa of beta(2)m, the contents of the alpha-helix, beta-sheet, turn, and random coil were 0, 45, 8, and 45aa, respectively. The SLA-2 protein displayed a typical alpha-helix structure while beta(2)m protein displayed a typical beta-sheet structure. Homology modeling of the SLA-2 and beta(2)m proteins demonstrated similarities with the structure of human and mouse MHC (major histocompatibility complex) class I proteins.

  6. Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models.

    Science.gov (United States)

    Leffler, Abba E; Kuryatov, Alexander; Zebroski, Henry A; Powell, Susan R; Filipenko, Petr; Hussein, Adel K; Gorson, Juliette; Heizmann, Anna; Lyskov, Sergey; Tsien, Richard W; Poget, Sébastien F; Nicke, Annette; Lindstrom, Jon; Rudy, Bernardo; Bonneau, Richard; Holford, Mandë

    2017-09-19

    Venom peptide toxins such as conotoxins play a critical role in the characterization of nicotinic acetylcholine receptor (nAChR) structure and function and have potential as nervous system therapeutics as well. However, the lack of solved structures of conotoxins bound to nAChRs and the large size of these peptides are barriers to their computational docking and design. We addressed these challenges in the context of the α4β2 nAChR, a widespread ligand-gated ion channel in the brain and a target for nicotine addiction therapy, and the 19-residue conotoxin α-GID that antagonizes it. We developed a docking algorithm, ToxDock, which used ensemble-docking and extensive conformational sampling to dock α-GID and its analogs to an α4β2 nAChR homology model. Experimental testing demonstrated that a virtual screen with ToxDock correctly identified three bioactive α-GID mutants (α-GID[A10V], α-GID[V13I], and α-GID[V13Y]) and one inactive variant (α-GID[A10Q]). Two mutants, α-GID[A10V] and α-GID[V13Y], had substantially reduced potency at the human α7 nAChR relative to α-GID, a desirable feature for α-GID analogs. The general usefulness of the docking algorithm was highlighted by redocking of peptide toxins to two ion channels and a binding protein in which the peptide toxins successfully reverted back to near-native crystallographic poses after being perturbed. Our results demonstrate that ToxDock can overcome two fundamental challenges of docking large toxin peptides to ion channel homology models, as exemplified by the α-GID:α4β2 nAChR complex, and is extendable to other toxin peptides and ion channels. ToxDock is freely available at rosie.rosettacommons.org/tox_dock.

  7. Homology modeling of 5-lipoxygenase and hints for better inhibitor design

    Science.gov (United States)

    Aparoy, P.; Reddy, R. N.; Guruprasad, Lalitha; Reddy, M. R.; Reddanna, P.

    2008-09-01

    Lipoxygenases (LOXs) are a group of enzymes involved in the oxygenation of polyunsaturated fatty acids. Among these 5-lipoxygenase (5-LOX) is the key enzyme leading to the formation of pharmacologically important leukotrienes and lipoxins, the mediators of inflammatory and allergic disorders. In view of close functional similarity to mammalian lipoxygenase, potato 5-LOX is used extensively. In this study, the homology modeling technique has been used to construct the structure of potato 5-LOX. The amino acid sequence identity between the target protein and sequence of template protein 1NO3 (soybean LOX-3) searched from NCBI protein BLAST was 63%. Based on the template structure, the protein model was constructed by using the Homology program in InsightII. The protein model was briefly refined by energy minimization steps and validated using Profile-3D, ERRAT and PROCHECK. The results showed that 99.3% of the amino acids were in allowed regions of Ramachandran plot, suggesting that the model is accurate and its stereochemical quality good. Like all LOXs, 5-LOX also has a two-domain structure, the small N-terminal β-barrel domain and a larger catalytic domain containing a single atom of non-heme iron coordinating with His525, His530, His716 and Ile864. Asn720 is present in the fifth coordination position of iron. The sixth coordination position faces the open cavity occupied here by the ligands which are docked. Our model of the enzyme is further validated by examining the interactions of earlier reported inhibitors and by energy minimization studies which were carried out using molecular mechanics calculations. Four ligands, nordihydroguaiaretic acid (NDGA) having IC50 of 1.5 μM and analogs of benzyl propargyl ethers having IC50 values of 760 μM, 45 μM, and no inhibition respectively were selected for our docking and energy minimization studies. Our results correlated well with the experimental data reported earlier, which proved the quality of the model. This

  8. DINAMO: a coupled sequence alignment editor/molecular graphics tool for interactive homology modeling of proteins.

    Science.gov (United States)

    Hansen, M; Bentz, J; Baucom, A; Gregoret, L

    1998-01-01

    Gaining functional information about a novel protein is a universal problem in biomedical research. With the explosive growth of the protein sequence and structural databases, it is becoming increasingly common for researchers to attempt to build a three-dimensional model of their protein of interest in order to gain information about its structure and interactions with other molecules. The two most reliable methods for predicting the structure of a protein are homology modeling, in which the novel sequence is modeled on the known three-dimensional structure of a related protein, and fold recognition (threading), where the sequence is scored against a library of fold models, and the highest scoring model is selected. The sequence alignment to a known structure can be ambiguous, and human intervention is often required to optimize the model. We describe an interactive model building and assessment tool in which a sequence alignment editor is dynamically coupled to a molecular graphics display. By means of a set of assessment tools, the user may optimize his or her alignment to satisfy the known heuristics of protein structure. Adjustments to the sequence alignment made by the user are reflected in the displayed model by color and other visual cues. For instance, residues are colored by hydrophobicity in both the three-dimensional model and in the sequence alignment. This aids the user in identifying undesirable buried polar residues. Several different evaluation metrics may be selected including residue conservation, residue properties, and visualization of predicted secondary structure. These characteristics may be mapped to the model both singly and in combination. DINAMO is a Java-based tool that may be run either over the web or installed locally. Its modular architecture also allows Java-literate users to add plug-ins of their own design.

  9. Gclust Server: 86157 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 86157 TET_11.m00460 Cluster Sequences Related Sequences(218) 1062 hypothetical prot...ein chr_0_8254747_11; no annotation 1 1.00e-25 0.0 11.11 0.0 0.0 0.0 0.0 Show 86157 Cluster ID 86157 Sequenc...e ID TET_11.m00460 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(2...4747_11; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-25 Plants and algae (7spe... Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR:

  10. Gclust Server: 5060 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 5060 TET_10.m00499 Cluster Sequences Related Sequences(35) 125 hypothetical protein... chr_0_8254582_10; no annotation 21 1.00e-10 0.0 11.11 0.0 0.0 0.0 0.0 Show 5060 Cluster ID 5060 Sequence ID... TET_10.m00499 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(35) S...0; no annotation Number of Sequences 21 Homologs 21 Clustering threshold 1.00e-10 Plants and algae (7species...ecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  11. Gclust Server: 129313 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 129313 PPT_166156 Cluster Sequences Related Sequences(6) 126 estExt_fgenesh1_pg.C_1...040010; no annotation 1 1.00e-60 14.29 0.0 0.0 0.0 0.0 0.0 Show 129313 Cluster ID 129313 Sequence ID PPT_166156 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(6) Sequence leng...er of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and algae (7species) (%) 14.29 Other Bikon...Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PPT: 1 Species not appearing in this clus

  12. Gclust Server: 25873 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 25873 NCR_NCU09641 Cluster Sequences Related Sequences(6) 711 hypothetical protein ...(translation) (712 aa); no annotation 4 1.00e-99 14.29 0.0 0.0 0.0 0.0 12.5 Show 25873 Cluster ID 25873 Sequ...ence ID NCR_NCU09641 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences...on) (712 aa); no annotation Number of Sequences 4 Homologs 4 Clustering threshold 1.00e-99 Plants and algae ...OSA: 1 NCR: 3 Species not appearing in this cluster ATH: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA:

  13. Gclust Server: 13108 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 13108 Npun1_NpF1634 Cluster Sequences Related Sequences(29) 167 hypothetical protei...n [Nostoc sp. PCC 7120] 8 1.00e-28 0.0 0.0 12.0 0.0 0.0 0.0 Show 13108 Cluster ID 13108 Sequence ID Npun1_NpF1634 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(29) Sequence l...mber of Sequences 8 Homologs 8 Clustering threshold 1.00e-28 Plants and algae (7species) (%) 0.0 Other Bikon...(Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species Ana: 2 Ava: 2 Npun: 4 Species not appearing in this clus

  14. Gclust Server: 19131 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 19131 PPT_100400 Cluster Sequences Related Sequences(392) 154 fgenesh1_pg.scaffold_...421000013; no annotation 5 1.00e-28 14.29 0.0 0.0 0.0 0.0 0.0 Show 19131 Cluster ID 19131 Sequence ID PPT_100400 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(392) Sequence l... Number of Sequences 5 Homologs 5 Clustering threshold 1.00e-28 Plants and algae (7species) (%) 14.29 Other ...nts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PPT: 5 Species not appearing in this clus

  15. Gclust Server: 36163 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 36163 NpunA_pNPAR046 Cluster Sequences Related Sequences(2) 230 ORF_ID:all8044~unkn...own protein [Nostoc sp. PCC 7120] 3 1.00e-40 0.0 0.0 8.0 0.0 0.0 0.0 Show 36163 Cluster ID 36163 Sequence ID... NpunA_pNPAR046 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(2) S...oc sp. PCC 7120] Number of Sequences 3 Homologs 3 Clustering threshold 1.00e-40 Plants and algae (7species) ... Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR:

  16. Gclust Server: 39265 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 39265 NCR_NCU02386 Cluster Sequences - 640 conserved hypothetical protein (translat...ion) (641 aa); no annotation 3 1.00e-60 0.0 0.0 0.0 0.0 0.0 12.5 Show 39265 Cluster ID 39265 Sequence ID NCR_NCU02386 Link to clus...ter sequences Cluster Sequences Link to related sequences - Sequence length 640 Repres...otation Number of Sequences 3 Homologs 3 Clustering threshold 1.00e-60 Plants and algae (7species) (%) 0.0 O...thokonts (Animals and fungi) (8species) (%) 12.5 Number of Sequences for each species NCR: 3 Species not appearing in this clus

  17. Gclust Server: 116418 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 116418 NCR_NCU00422 Cluster Sequences Related Sequences(36) 410 hypothetical protei...n similar to curved DNA-binding protein (translation) (411 aa); no annotation 1 1.00e-45 0.0 0.0 0.0 0.0 0.0 12.5 Show 116418 Clus...ter ID 116418 Sequence ID NCR_NCU00422 Link to cluster sequences Cluster Sequences Lin...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-45 Plants and algae (7species) (%) 0.0 Other Biko...(Animals and fungi) (8species) (%) 12.5 Number of Sequences for each species NCR: 1 Species not appearing in this clus

  18. Gclust Server: 25482 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 25482 PHRA_84464 Cluster Sequences Related Sequences(7) 1029 fgenesh1_pg.C_scaffold..._114000003; no annotation 4 1.00e-99 0.0 44.44 0.0 0.0 0.0 0.0 Show 25482 Cluster ID 25482 Sequence ID PHRA_84464 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(7) Sequence le...on Number of Sequences 4 Homologs 4 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other ...: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 T

  19. Gclust Server: 70552 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 70552 Sme_SMa1998 Cluster Sequences Related Sequences(314) 497 Putative ABC transpo...rter, ATP-binding protein 1 1.00e-60 0.0 0.0 0.0 0.0 3.23 0.0 Show 70552 Cluster ID 70552 Sequence ID Sme_SMa1998 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(314) Sequence ...n Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-60 Plants and algae (7species) (%) 0.0 Other B...nts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species Sme: 1 Species not appearing in this clus

  20. Gclust Server: 89202 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 89202 TET_87.m00193 Cluster Sequences Related Sequences(255) 402 Protein kinase dom...ain containing protein chr_0_8254479_87; no annotation 1 1.00e-45 0.0 11.11 0.0 0.0 0.0 0.0 Show 89202 Clust...er ID 89202 Sequence ID TET_87.m00193 Link to cluster sequences Cluster Sequences Link to related sequences ...se domain containing protein chr_0_8254479_87; no annotation Number of Sequences 1 Homologs 1 Clustering thr...r of Sequences for each species TET: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CR

  1. Gclust Server: 97379 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 97379 DME_CG17732_24667113 Cluster Sequences Related Sequences(200) 720 CG17732: CG...17732-PA 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 97379 Cluster ID 97379 Sequence ID DME_CG17732_24667113 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(200) Sequence length 7...20 Representative annotation CG17732: CG17732-PA Number of Sequences 1 Homologs 1 Clus...(%) 12.5 Number of Sequences for each species DME: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoT

  2. Gclust Server: 115082 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 115082 Fal_FRAAL4041 Cluster Sequences Related Sequences(42) 309 putative Rieske Fe...-S membrane protein 1 1.00e-40 0.0 0.0 0.0 0.0 3.23 0.0 Show 115082 Cluster ID 115082 Sequence ID Fal_FRAAL4041 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(42) Sequence len... Sequences 1 Homologs 1 Clustering threshold 1.00e-40 Plants and algae (7species) (%) 0.0 Other Bikonts (Chr...s and fungi) (8species) (%) 0.0 Number of Sequences for each species Fal: 1 Species not appearing in this clus

  3. Gclust Server: 50440 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 50440 HSA_113426210 Cluster Sequences Related Sequences(1) 847 XP_063871.8 PREDICTE...D: hypothetical protein ; no annotation 2 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 50440 Cluster ID 50440 Sequ...ence ID HSA_113426210 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequence...tical protein ; no annotation Number of Sequences 2 Homologs 2 Clustering threshold 1.00e-99 Plants and alga...HSA: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA:

  4. Gclust Server: 83299 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 83299 Rde_RD1_3099 Cluster Sequences Related Sequences(288) 260 ABC transporter, AT...P-binding protein, putative 1 1.00e-80 0.0 0.0 0.0 6.67 0.0 0.0 Show 83299 Cluster ID 83299 Sequence ID Rde_RD1_3099 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(288) Sequen...ative Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-80 Plants and algae (7species) (%) 0.0 Oth...hokonts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species Rde: 1 Species not appearing in this clus

  5. Gclust Server: 3749 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 3749 PHSO_108140 Cluster Sequences Related Sequences(40) 255 estExt_fgenesh1_pm.C_1...0005; no annotation 27 1.00e-31 100.0 77.78 0.0 0.0 0.0 75.0 Show 3749 Cluster ID 3749 Sequence ID PHSO_108140 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(40) Sequence leng... of Sequences 27 Homologs 27 Clustering threshold 1.00e-31 Plants and algae (7species) (%) 100.0 Other Bikon...1 HSA: 1 Species not appearing in this cluster GTH: 0 Ter: 0 Ana: 0 Ava: 0 Npun:

  6. Gclust Server: 71744 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 71744 PPT_92540 Cluster Sequences Related Sequences(427) 486 fgenesh1_pg.scaffold_2...26000062; no annotation 1 1.00e-16 14.29 0.0 0.0 0.0 0.0 0.0 Show 71744 Cluster ID 71744 Sequence ID PPT_92540 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(427) Sequence len...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-16 Plants and algae (7species) (%) 14.29 Other Bi...s (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PPT: 1 Species not appearing in this clus

  7. Gclust Server: 40474 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 40474 DME_CG41105_116007212 Cluster Sequences Related Sequences(230) 341 CG41105: C...G41105-PA, isoform A 2 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 40474 Cluster ID 40474 Sequence ID DME_CG41105_116007212 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(230) Sequ...f Sequences 2 Homologs 2 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Bikonts (Ch...s and fungi) (8species) (%) 12.5 Number of Sequences for each species DME: 2 Species not appearing in this clus

  8. Gclust Server: 91821 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 91821 CRE_196685=CYP740A1 Cluster Sequences - 556 cytochrome P450, unkown function,... in CYP85 clanno annotation 1 1.00e+00 14.29 0.0 0.0 0.0 0.0 0.0 Show 91821 Cluster ID 91821 Sequence ID CRE..._196685=CYP740A1 Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 556...tation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e+00 Plants and algae (7species) (%) 14.29 ...sthokonts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species CRE: 1 Species not appearing in this clus

  9. Gclust Server: 19906 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 19906 PHRA_76699 Cluster Sequences Related Sequences(44) 142 fgenesh1_pg.C_scaffold..._19000131; no annotation 5 1.00e-25 0.0 22.22 0.0 0.0 0.0 0.0 Show 19906 Cluster ID 19906 Sequence ID PHRA_76699 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(44) Sequence le... Number of Sequences 5 Homologs 5 Clustering threshold 1.00e-25 Plants and algae (7species) (%) 0.0 Other Bi...nts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PHRA: 3 PHSO: 2 Species not appearing in this clus

  10. Gclust Server: 5507 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 5507 Atu_Atu3260 Cluster Sequences Related Sequences(140) 332 ABC transporter, subs...trate binding protein [C4-dicarboxylate] 19 1.00e-12 0.0 0.0 0.0 20.0 25.81 0.0 Show 5507 Cluster ID 5507 Se...quence ID Atu_Atu3260 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequence...inding protein [C4-dicarboxylate] Number of Sequences 19 Homologs 19 Clustering threshold 1.00e-12 Plants an...species Atu: 1 Bja: 2 Ccr: 1 Mes: 1 Rhe: 1 Rle: 3 Sme: 5 Rde: 2 Rsh: 1 Rsp: 1 Vvy: 1 Species not appearing in this clus

  11. Gclust Server: 118689 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 118689 NCR_NCU04112 Cluster Sequences Related Sequences(27) 1565 hypothetical prote...in (translation) (1566 aa); no annotation 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 118689 Cluster ID 118689 ...Sequence ID NCR_NCU04112 Link to cluster sequences Cluster Sequences Link to related sequences Related Seque...nslation) (1566 aa); no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and...cies NCR: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0

  12. Gclust Server: 1567 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 1567 Atu_Atu2796=cobM Cluster Sequences Related Sequences(251) 257 precorrin-4 C11-...methyltransferase 53 1.00e-19 0.0 0.0 100.0 80.0 51.61 0.0 Show 1567 Cluster ID 1567 Sequence ID Atu_Atu2796=cobM Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(251) Sequence ...Sequences 53 Homologs 53 Clustering threshold 1.00e-19 Plants and algae (7species) (%) 0.0 Other Bikonts (Ch...Bma: 1 Caur: 1 Clim: 1 Ctep: 1 Afu: 1 Mac: 1 Ape: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR

  13. Gclust Server: 31029 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 31029 ATH_AT2G18370_15224163 Cluster Sequences Related Sequences(54) 116 protease i...nhibitor/seed storage/lipid transfer protein (LTP) family protein 3 1.00e-60 42.86 0.0 0.0 0.0 0.0 0.0 Show 31029 Clus...ter ID 31029 Sequence ID ATH_AT2G18370_15224163 Link to cluster sequences Cluster Sequences Link t...tation protease inhibitor/seed storage/lipid transfer protein (LTP) family protein Number of Sequences 3 Homologs 3 Clus...species) (%) 0.0 Number of Sequences for each species ATH: 1 OSA: 1 PoTR: 1 Species not appearing in this clus

  14. Gclust Server: 80322 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 80322 TET_305.m00018 Cluster Sequences Related Sequences(300) 886 cyclic nucleotide...-binding domain containing protein chr_0_8254500_305; no annotation 1 1.00e-80 0.0 11.11 0.0 0.0 0.0 0.0 Show 80322 Clus...ter ID 80322 Sequence ID TET_305.m00018 Link to cluster sequences Cluster Sequences Link to rela...n cyclic nucleotide-binding domain containing protein chr_0_8254500_305; no annotation Number of Sequences 1 Homologs 1 Clus...) (8species) (%) 0.0 Number of Sequences for each species TET: 1 Species not appearing in this cluster ATH:

  15. Gclust Server: 16076 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 16076 HSA_113421619 Cluster Sequences Related Sequences(421) 309 XP_001131415.1 PRE...DICTED: hypothetical protein ; no annotation 6 1.00e-06 0.0 0.0 0.0 0.0 0.0 50.0 Show 16076 Cluster ID 16076... Sequence ID HSA_113421619 Link to cluster sequences Cluster Sequences Link to related sequences Related Seq...D: hypothetical protein ; no annotation Number of Sequences 6 Homologs 6 Clustering threshold 1.00e-06 Plant...h species SCE: 1 NCR: 1 HSA: 3 CEL: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE

  16. Gclust Server: 116121 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 116121 NGR_71688 Cluster Sequences Related Sequences(37) 142 fgeneshNG_pg.scaffold_...48000075; no annotation 1 1.00e-70 0.0 11.11 0.0 0.0 0.0 0.0 Show 116121 Cluster ID 116121 Sequence ID NGR_71688 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(37) Sequence le...Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-70 Plants and algae (7species) (%) 0.0 Other Bik...ts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species NGR: 1 Species not appearing in this clus

  17. Gclust Server: 87454 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 87454 PPT_87253 Cluster Sequences Related Sequences(261) 207 fgenesh1_pg.scaffold_1...56000002; no annotation 1 1.00e-99 14.29 0.0 0.0 0.0 0.0 0.0 Show 87454 Cluster ID 87454 Sequence ID PPT_87253 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(261) Sequence len...umber of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 14.29 Other Bi...s (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PPT: 1 Species not appearing in this clus

  18. Gclust Server: 90711 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 90711 PPT_70666 Cluster Sequences Related Sequences(252) 114 fgenesh1_pg.scaffold_2...9000033; no annotation 1 9.98e-01 14.29 0.0 0.0 0.0 0.0 0.0 Show 90711 Cluster ID 90711 Sequence ID PPT_70666 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(252) Sequence leng...ber of Sequences 1 Homologs 1 Clustering threshold 9.98e-01 Plants and algae (7species) (%) 14.29 Other Biko...(Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PPT: 1 Species not appearing in this clus

  19. Gclust Server: 65616 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 65616 PHSO_143668 Cluster Sequences Related Sequences(959) 1016 estExt_fgenesh1_pg....C_1470016; no annotation 1 1.00e-70 0.0 11.11 0.0 0.0 0.0 0.0 Show 65616 Cluster ID 65616 Sequence ID PHSO_143668 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(959) Sequence ... Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-70 Plants and algae (7species) (%) 0.0 Other Bi...nts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PHSO: 1 Species not appearing in this clus

  20. Gclust Server: 66336 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 66336 TET_44.m00293 Cluster Sequences - 1164 Protein kinase domain containing prote...in chr_0_8254555_44; no annotation 1 1.00e+00 0.0 11.11 0.0 0.0 0.0 0.0 Show 66336 Cluster ID 66336 Sequence... ID TET_44.m00293 Link to cluster sequences Cluster Sequences Link to related sequences - Sequence length 11...55_44; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e+00 Plants and algae (7speci...pecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  1. Gclust Server: 33266 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 33266 DME_CG9415_28573590 Cluster Sequences Related Sequences(5) 488 Xbp1: X box bi...nding protein-1 CG9415-PB, isoform B 3 1.00e-90 0.0 0.0 0.0 0.0 0.0 25.0 Show 33266 Cluster ID 33266 Sequenc...e ID DME_CG9415_28573590 Link to cluster sequences Cluster Sequences Link to related sequences Related Seque...-1 CG9415-PB, isoform B Number of Sequences 3 Homologs 3 Clustering threshold 1.00e-90 Plants and algae (7sp... CEL: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA:

  2. Gclust Server: 73433 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 73433 PPT_81552 Cluster Sequences Related Sequences(390) 541 fgenesh1_pg.scaffold_9...6000057; no annotation 1 1.00e-12 14.29 0.0 0.0 0.0 0.0 0.0 Show 73433 Cluster ID 73433 Sequence ID PPT_81552 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(390) Sequence leng...ber of Sequences 1 Homologs 1 Clustering threshold 1.00e-12 Plants and algae (7species) (%) 14.29 Other Biko...(Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PPT: 1 Species not appearing in this clus

  3. Gclust Server: 14104 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 14104 Fal_FRAAL1960 Cluster Sequences Related Sequences(291) 492 putative two-compo...nent sensor histidine kinase 7 1.00e-25 0.0 0.0 8.0 0.0 9.68 0.0 Show 14104 Cluster ID 14104 Sequence ID Fal_FRAAL1960 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(291) Sequ... kinase Number of Sequences 7 Homologs 7 Clustering threshold 1.00e-25 Plants and algae (7species) (%) 0.0 O...Fal: 1 Sco: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH:

  4. Gclust Server: 77264 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 77264 Gox_GOX0105 Cluster Sequences Related Sequences(333) 700 Protein Translation ...Elongation Factor G (EF-G) 1 1.00e-45 0.0 0.0 0.0 0.0 3.23 0.0 Show 77264 Cluster ID 77264 Sequence ID Gox_GOX0105 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(333) Sequence...-G) Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-45 Plants and algae (7species) (%) 0.0 Other...konts (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species Gox: 1 Species not appearing in this clus

  5. Gclust Server: 99248 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 99248 NGR_79829 Cluster Sequences Related Sequences(171) 760 estExt_fgeneshNG_pg.C_...250066; no annotation 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 99248 Cluster ID 99248 Sequence ID NGR_79829 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(171) Sequence lengt...r of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Bikonts ...nimals and fungi) (8species) (%) 0.0 Number of Sequences for each species NGR: 1 Species not appearing in this clus

  6. Gclust Server: 94832 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 94832 Bsu_BSU28110=spoVID Cluster Sequences Related Sequences(211) 575 required for... assembly of the spore coat (stage VI sporulation) 1 1.00e-99 0.0 0.0 0.0 0.0 3.23 0.0 Show 94832 Cluster ID... 94832 Sequence ID Bsu_BSU28110=spoVID Link to cluster sequences Cluster Sequences Link to related sequences...r assembly of the spore coat (stage VI sporulation) Number of Sequences 1 Homologs 1 Clustering threshold 1....nces for each species Bsu: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU:

  7. Gclust Server: 86949 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 86949 CME_CME050C Cluster Sequences Related Sequences(267) 431 similar to nuclear L...IM interactor-interacting factor 1 1.00e-22 14.29 0.0 0.0 0.0 0.0 0.0 Show 86949 Cluster ID 86949 Sequence I...D CME_CME050C Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(267) S...teracting factor Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-22 Plants and algae (7species) ...es not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 GTH: 0 PFA: 0 PTR: 0 TPS: 0 Ter

  8. Gclust Server: 77743 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 77743 CEL_T08B2.2_17508941 Cluster Sequences Related Sequences(252) 321 col-56: COL...lagen family member (col-56) 1 1.00e-19 0.0 0.0 0.0 0.0 0.0 12.5 Show 77743 Cluster ID 77743 Sequence ID CEL..._T08B2.2_17508941 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(25...col-56) Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-19 Plants and algae (7species) (%) 0.0 O...thokonts (Animals and fungi) (8species) (%) 12.5 Number of Sequences for each species CEL: 1 Species not appearing in this clus

  9. Gclust Server: 102371 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 102371 HSA_39777614 Cluster Sequences Related Sequences(134) 396 NP_945173.1 SS18-l...ike protein 1 ; no annotation 1 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 102371 Cluster ID 102371 Sequence ID ...HSA_39777614 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(134) Se...annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0....pisthokonts (Animals and fungi) (8species) (%) 12.5 Number of Sequences for each species HSA: 1 Species not appearing in this clus

  10. Gclust Server: 12829 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 12829 DME_CG1839_18859805 Cluster Sequences Related Sequences(136) 669 CG1839: CG18...39-PA 8 1.00e-70 28.57 11.11 0.0 0.0 0.0 62.5 Show 12829 Cluster ID 12829 Sequence ID DME_CG1839_18859805 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(136) Sequence length 6...69 Representative annotation CG1839: CG1839-PA Number of Sequences 8 Homologs 8 Clus...ecies not appearing in this cluster OSA: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0 TPS: 0 Ter: 0 A

  11. Gclust Server: 125006 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 125006 NGR_59308 Cluster Sequences Related Sequences(12) 456 estExt_fgeneshHS_pg.C_...570025; no annotation 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 125006 Cluster ID 125006 Sequence ID NGR_59308 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(12) Sequence leng...er of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Bikonts...Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species NGR: 1 Species not appearing in this clus

  12. Gclust Server: 74755 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 74755 ATH_AT2G05940_15225019 Cluster Sequences Related Sequences(385) 462 protein k...inase, putative 1 1.00e-45 14.29 0.0 0.0 0.0 0.0 0.0 Show 74755 Cluster ID 74755 Sequence ID ATH_AT2G05940_15225019 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(385) Sequenc...e length 462 Representative annotation protein kinase, putative Number of Sequences 1 Homologs 1 Clus...ungi) (8species) (%) 0.0 Number of Sequences for each species ATH: 1 Species not appearing in this cluster O

  13. Gclust Server: 93769 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 93769 TET_30.m00259 Cluster Sequences Related Sequences(225) 235 hypothetical prote...in chr_0_8254431_30; no annotation 1 1.00e-99 0.0 11.11 0.0 0.0 0.0 0.0 Show 93769 Cluster ID 93769 Sequence... ID TET_30.m00259 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(22...31_30; no annotation Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-99 Plants and algae (7speci...pecies not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0 PTR: 0

  14. Gclust Server: 52069 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 52069 HSA_88943616 Cluster Sequences Related Sequences(1) 320 XP_939303.1 PREDICTED...: hypothetical protein ; no annotation 2 1.00e-99 0.0 0.0 0.0 0.0 0.0 12.5 Show 52069 Cluster ID 52069 Seque...nce ID HSA_88943616 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(...cal protein ; no annotation Number of Sequences 2 Homologs 2 Clustering threshold 1.00e-99 Plants and algae ...A: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0 PFA: 0

  15. Gclust Server: 73420 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 73420 HSA_113426901 Cluster Sequences Related Sequences(154) 159 XP_001127218.1 PRE...DICTED: similar to keratin associated protein 9.2 ; no annotation 1 1.00e-31 0.0 0.0 0.0 0.0 0.0 12.5 Show 73420 Clus...ter ID 73420 Sequence ID HSA_113426901 Link to cluster sequences Cluster Sequences Link to related ..._001127218.1 PREDICTED: similar to keratin associated protein 9.2 ; no annotation Number of Sequences 1 Homologs 1 Clus...cies) (%) 12.5 Number of Sequences for each species HSA: 1 Species not appearing in this cluster ATH: 0 OSA:

  16. Gclust Server: 86804 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 86804 Pst_PSPTO_2988 Cluster Sequences Related Sequences(265) 355 branched-chain am...ino acid ABC transporter, permease protein 1 1.00e-31 0.0 0.0 0.0 0.0 3.23 0.0 Show 86804 Cluster ID 86804 S...equence ID Pst_PSPTO_2988 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequ...d ABC transporter, permease protein Number of Sequences 1 Homologs 1 Clustering threshold 1.00e-31 Plants an...ecies Pst: 1 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 PPT: 0 CRE: 0 OTAU: 0 CME: 0 GTH: 0

  17. Gclust Server: 8699 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 8699 CRE_189183=FAP53 Cluster Sequences Related Sequences(366) 310 Flagellar Associ...ated Proteinno annotation 12 1.00e-12 42.86 33.33 0.0 0.0 0.0 25.0 Show 8699 Cluster ID 8699 Sequence ID CRE..._189183=FAP53 Link to cluster sequences Cluster Sequences Link to related sequences Related Sequences(366) S...ation Number of Sequences 12 Homologs 12 Clustering threshold 1.00e-12 Plants and algae (7species) (%) 42.86...: 1 TPS: 1 PHRA: 2 PHSO: 1 HSA: 1 DME: 2 Species not appearing in this cluster ATH: 0 OSA: 0 PoTR: 0 CME: 0

  18. Gclust Server: 126403 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 126403 ATH_AT4G12360_15234524 Cluster Sequences Related Sequences(10) 161 protease ...inhibitor/seed storage/lipid transfer protein (LTP) family protein 1 1.00e-80 14.29 0.0 0.0 0.0 0.0 0.0 Show 126403 Clus...ter ID 126403 Sequence ID ATH_AT4G12360_15234524 Link to cluster sequences Cluster Sequences Lin...nnotation protease inhibitor/seed storage/lipid transfer protein (LTP) family protein Number of Sequences 1 Homologs 1 Clus... (8species) (%) 0.0 Number of Sequences for each species ATH: 1 Species not appearing in this cluster OSA: 0

  19. Gclust Server: 24363 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 24363 ATH_AT1G64500_15217659 Cluster Sequences Related Sequences(53) 368 glutaredox...in family protein 4 1.00e-60 42.86 0.0 0.0 0.0 0.0 0.0 Show 24363 Cluster ID 24363 Sequence ID ATH_AT1G64500_15217659 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(53) Sequen...ce length 368 Representative annotation glutaredoxin family protein Number of Sequences 4 Homologs 4 Clus...nd fungi) (8species) (%) 0.0 Number of Sequences for each species ATH: 1 OSA: 1 PoTR: 2 Species not appearing in this clus

  20. Gclust Server: 46738 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 46738 PHRA_74760 Cluster Sequences Related Sequences(16) 496 fgenesh1_pg.C_scaffold..._9000163; no annotation 2 1.00e-99 0.0 22.22 0.0 0.0 0.0 0.0 Show 46738 Cluster ID 46738 Sequence ID PHRA_74760 Link to clus...ter sequences Cluster Sequences Link to related sequences Related Sequences(16) Sequence len...umber of Sequences 2 Homologs 2 Clustering threshold 1.00e-99 Plants and algae (7species) (%) 0.0 Other Biko...s (Animals and fungi) (8species) (%) 0.0 Number of Sequences for each species PHRA: 1 PHSO: 1 Species not appearing in this clus