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SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages...

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Autores principales: Biasini, Marco, Bienert, Stefan, Waterhouse, Andrew, Arnold, Konstantin, Studer, Gabriel, Schmidt, Tobias, Kiefer, Florian, Cassarino, Tiziano Gallo, Bertoni, Martino, Bordoli, Lorenza, Schwede, Torsten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086089/
https://www.ncbi.nlm.nih.gov/pubmed/24782522
http://dx.doi.org/10.1093/nar/gku340
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author Biasini, Marco
Bienert, Stefan
Waterhouse, Andrew
Arnold, Konstantin
Studer, Gabriel
Schmidt, Tobias
Kiefer, Florian
Cassarino, Tiziano Gallo
Bertoni, Martino
Bordoli, Lorenza
Schwede, Torsten
author_facet Biasini, Marco
Bienert, Stefan
Waterhouse, Andrew
Arnold, Konstantin
Studer, Gabriel
Schmidt, Tobias
Kiefer, Florian
Cassarino, Tiziano Gallo
Bertoni, Martino
Bordoli, Lorenza
Schwede, Torsten
author_sort Biasini, Marco
collection PubMed
description Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/.
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spelling pubmed-40860892014-10-28 SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information Biasini, Marco Bienert, Stefan Waterhouse, Andrew Arnold, Konstantin Studer, Gabriel Schmidt, Tobias Kiefer, Florian Cassarino, Tiziano Gallo Bertoni, Martino Bordoli, Lorenza Schwede, Torsten Nucleic Acids Res Article Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/. Oxford University Press 2014-07-01 2014-04-29 /pmc/articles/PMC4086089/ /pubmed/24782522 http://dx.doi.org/10.1093/nar/gku340 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Biasini, Marco
Bienert, Stefan
Waterhouse, Andrew
Arnold, Konstantin
Studer, Gabriel
Schmidt, Tobias
Kiefer, Florian
Cassarino, Tiziano Gallo
Bertoni, Martino
Bordoli, Lorenza
Schwede, Torsten
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
title SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
title_full SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
title_fullStr SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
title_full_unstemmed SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
title_short SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
title_sort swiss-model: modelling protein tertiary and quaternary structure using evolutionary information
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086089/
https://www.ncbi.nlm.nih.gov/pubmed/24782522
http://dx.doi.org/10.1093/nar/gku340
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