The Experts below are selected from a list of 84708 Experts worldwide ranked by ideXlab platform
Michael J.e. Sternberg - One of the best experts on this subject based on the ideXlab platform.
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the phyre2 web portal for Protein Modeling prediction and analysis
Nature Protocols, 2015Co-Authors: Lawrence A. Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J.e. SternbergAbstract:Phyre2 is a suite of tools available on the web to predict and analyze Protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art Protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's Protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a Protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a Protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for Proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission.
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The Phyre2 web portal for Protein Modeling, prediction and analysis
Nature Protocols, 2015Co-Authors: Lawrence A. Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J.e. SternbergAbstract:Phyre2 is a suite of tools available on the web to predict and analyze Protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art Protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols . In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's Protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a Protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a Protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for Proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2 . A typical structure prediction will be returned between 30 min and 2 h after submission. Phyre2 is a web-based tool for predicting and analyzing Protein structure and function. Phyre2 uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyze amino acid variants in a Protein sequence.
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Enhancement of Protein Modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
Proteins: Structure Function and Genetics, 2001Co-Authors: Paul A. Bates, Lawrence A. Kelley, R M Maccallum, Michael J.e. SternbergAbstract:Fourteen models were constructed andanalyzedfor the comparative Modeling sectionof Critical Assessment of Techniques for Protein Structure Prediction (CASP4). Sequence identity between each target and the best possible parent(s) ranged between 55 and 13%, and the root-mean-square deviation between model and target was from0.8 to 17.9 Å. In the fold recognition section, 10 of the 11 remote homologues were recognized. The Modeling protocols areacombinationof automatedcomputer algorithms, 3D-JIGSAW(for comparativeModeling) and3D-PSSM (for fold recognition), with human intervention at certain critical stages. In particular, intervention is required to check superfamily assignment, best possible parents from which to model, sequence alignments tothose parents andtake-off regions for Modeling variable regions. There now is a convergence of algorithms for comparative Modeling and fold recognition, particularly in the region of remote homology.
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enhancement of Protein Modeling by human intervention in applying the automatic programs 3d jigsaw and 3d pssm
Proteins, 2001Co-Authors: Paul A. Bates, Lawrence A. Kelley, R M Maccallum, Michael J.e. SternbergAbstract:Fourteen models were constructed and analyzed for the comparative Modeling section of Critical Assessment of Techniques for Protein Structure Prediction (CASP4). Sequence identity between each target and the best possible parent(s) ranged between 55 and 13%, and the root-mean-square deviation between model and target was from 0.8 to 17.9 A. In the fold recognition section, 10 of the 11 remote homologues were recognized. The Modeling protocols are a combination of automated computer algorithms, 3D-JIGSAW (for comparative Modeling) and 3D-PSSM (for fold recognition), with human intervention at certain critical stages. In particular, intervention is required to check superfamily assignment, best possible parents from which to model, sequence alignments to those parents and take-off regions for Modeling variable regions. There now is a convergence of algorithms for comparative Modeling and fold recognition, particularly in the region of remote homology. Proteins 2001;Suppl 5:39–46. © 2002 Wiley-Liss, Inc.
Manuel C Peitsch - One of the best experts on this subject based on the ideXlab platform.
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automated comparative Protein structure Modeling with swiss model and swiss pdbviewer a historical perspective
Electrophoresis, 2009Co-Authors: Nicolas Guex, T. Schwede, Manuel C PeitschAbstract:SWISS-MODEL pioneered the field of automated Modeling as the first Protein Modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and Modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative Protein Modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.
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large scale Protein Modeling and model repository
Intelligent Systems in Molecular Biology, 1997Co-Authors: Manuel C PeitschAbstract:Knowledge-based molecular modelling of Proteins has proven useful in many instances including the rational design of mutagenesis experiments, but it has been generally limited by the availability of expensive computer hardware and software. To overcome these limitations, we have developed the SWISS-MODEL server for automated knowledge-based Protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates Protein models for sequences which share significant similarities with at least one Protein of known 3D-structure. We now use the software framework of the server to generate large collections of Protein models. To store these models, we have established the SWISS-MODEL Repository, a new database for Protein models generated by theoretical approaches. This repository is directly integrated with SWISS-PROT and other databases through the ExPASy World-Wide Web server (URL is http://www.expasy.ch).
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swiss model and the swiss pdb viewer an environment for comparative Protein Modeling
Electrophoresis, 1997Co-Authors: Nicolas Gue, Manuel C PeitschAbstract:Comparative Protein Modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative Protein Modeling that consists of SWISS-MODEL, a server for automated comparative Protein Modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated Protein models. By making such tools freely available to the scientific community, we hope to increase the use of Protein structures and models in the process of experiment design.
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swiss model and the swiss pdbviewer an environment for comparative Protein Modeling
Electrophoresis, 1997Co-Authors: Nicolas Guex, Manuel C PeitschAbstract:Comparative Protein Modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative Protein Modeling that consists of SWISS-MODEL, a server for automated comparative Protein Modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated Protein models. By making such tools freely available to the scientific community, we hope to increase the use of Protein structures and models in the process of experiment design.
Lawrence A. Kelley - One of the best experts on this subject based on the ideXlab platform.
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the phyre2 web portal for Protein Modeling prediction and analysis
Nature Protocols, 2015Co-Authors: Lawrence A. Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J.e. SternbergAbstract:Phyre2 is a suite of tools available on the web to predict and analyze Protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art Protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's Protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a Protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a Protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for Proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission.
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The Phyre2 web portal for Protein Modeling, prediction and analysis
Nature Protocols, 2015Co-Authors: Lawrence A. Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J.e. SternbergAbstract:Phyre2 is a suite of tools available on the web to predict and analyze Protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art Protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols . In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's Protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a Protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a Protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for Proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2 . A typical structure prediction will be returned between 30 min and 2 h after submission. Phyre2 is a web-based tool for predicting and analyzing Protein structure and function. Phyre2 uses advanced remote homology detection methods to build 3D models, predict ligand binding sites, and analyze amino acid variants in a Protein sequence.
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Enhancement of Protein Modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
Proteins: Structure Function and Genetics, 2001Co-Authors: Paul A. Bates, Lawrence A. Kelley, R M Maccallum, Michael J.e. SternbergAbstract:Fourteen models were constructed andanalyzedfor the comparative Modeling sectionof Critical Assessment of Techniques for Protein Structure Prediction (CASP4). Sequence identity between each target and the best possible parent(s) ranged between 55 and 13%, and the root-mean-square deviation between model and target was from0.8 to 17.9 Å. In the fold recognition section, 10 of the 11 remote homologues were recognized. The Modeling protocols areacombinationof automatedcomputer algorithms, 3D-JIGSAW(for comparativeModeling) and3D-PSSM (for fold recognition), with human intervention at certain critical stages. In particular, intervention is required to check superfamily assignment, best possible parents from which to model, sequence alignments tothose parents andtake-off regions for Modeling variable regions. There now is a convergence of algorithms for comparative Modeling and fold recognition, particularly in the region of remote homology.
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enhancement of Protein Modeling by human intervention in applying the automatic programs 3d jigsaw and 3d pssm
Proteins, 2001Co-Authors: Paul A. Bates, Lawrence A. Kelley, R M Maccallum, Michael J.e. SternbergAbstract:Fourteen models were constructed and analyzed for the comparative Modeling section of Critical Assessment of Techniques for Protein Structure Prediction (CASP4). Sequence identity between each target and the best possible parent(s) ranged between 55 and 13%, and the root-mean-square deviation between model and target was from 0.8 to 17.9 A. In the fold recognition section, 10 of the 11 remote homologues were recognized. The Modeling protocols are a combination of automated computer algorithms, 3D-JIGSAW (for comparative Modeling) and 3D-PSSM (for fold recognition), with human intervention at certain critical stages. In particular, intervention is required to check superfamily assignment, best possible parents from which to model, sequence alignments to those parents and take-off regions for Modeling variable regions. There now is a convergence of algorithms for comparative Modeling and fold recognition, particularly in the region of remote homology. Proteins 2001;Suppl 5:39–46. © 2002 Wiley-Liss, Inc.
Nicolas Guex - One of the best experts on this subject based on the ideXlab platform.
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automated comparative Protein structure Modeling with swiss model and swiss pdbviewer a historical perspective
Electrophoresis, 2009Co-Authors: Nicolas Guex, T. Schwede, Manuel C PeitschAbstract:SWISS-MODEL pioneered the field of automated Modeling as the first Protein Modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and Modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative Protein Modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.
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a geographic variant of the staphylococcus aureus panton valentine leukocidin toxin and the origin of community associated methicillin resistant s aureus usa300
The Journal of Infectious Diseases, 2008Co-Authors: Patrick F Ohara, Nicolas Guex, Michael J Word, Linda A Miller, Julie A Becker, Stacey L Walsh, Nicole Scangarella, Joshua West, Ribhi Shawar, Heather AmrinemadsenAbstract:Background. The majority of recent community-associated methicillin-resistant Staphylococcus aureus (MRSA) infections in the United States have been caused by a single clone, USA300. USA300 secretes Panton-Valentine leukocidin (PVL) toxin, which is associated with highly virulent infections. Methods. We sequenced the PVL genes of 174 S. aureus isolates from a global clinical sample. We combined phylogenetic reconstruction and Protein Modeling methods to analyze genetic variation in PVL. Results. Nucleotide variation was detected at 12 of 1726 sites. Two PVL sequence variants, the R variant and the H variant, were identified on the basis of a substitution at nt 527. Of sequences obtained in the United States, 96.7% harbor the R variant, whereas 95.6% of sequences obtained outside the United States harbor the H variant; 91.3% of MRSA isolates harbor the R variant, and 91.3% of methicillin-susceptible strains harbor the H variant. A molecular model of PVL shows 3 mechanisms by which the amino acid substitution may affect PVL function. Conclusions. All sampled PVL genes appear to share a recent common ancestor and spread via a combination of clonal expansion and horizontal transfer. US isolates harbor a variant of PVL that is strongly associated with MRSA infections. Protein Modeling reveals that this variant may have functional significance. We propose a hypothesis for the origin of USA300.
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swiss model and the swiss pdbviewer an environment for comparative Protein Modeling
Electrophoresis, 1997Co-Authors: Nicolas Guex, Manuel C PeitschAbstract:Comparative Protein Modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative Protein Modeling that consists of SWISS-MODEL, a server for automated comparative Protein Modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated Protein models. By making such tools freely available to the scientific community, we hope to increase the use of Protein structures and models in the process of experiment design.
T. Schwede - One of the best experts on this subject based on the ideXlab platform.
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automated comparative Protein structure Modeling with swiss model and swiss pdbviewer a historical perspective
Electrophoresis, 2009Co-Authors: Nicolas Guex, T. Schwede, Manuel C PeitschAbstract:SWISS-MODEL pioneered the field of automated Modeling as the first Protein Modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and Modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative Protein Modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.
