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CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex w...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031000/ https://www.ncbi.nlm.nih.gov/pubmed/29762700 http://dx.doi.org/10.1093/nar/gky356 |
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author | Kuriata, Aleksander Gierut, Aleksandra Maria Oleniecki, Tymoteusz Ciemny, Maciej Paweł Kolinski, Andrzej Kurcinski, Mateusz Kmiecik, Sebastian |
author_facet | Kuriata, Aleksander Gierut, Aleksandra Maria Oleniecki, Tymoteusz Ciemny, Maciej Paweł Kolinski, Andrzej Kurcinski, Mateusz Kmiecik, Sebastian |
author_sort | Kuriata, Aleksander |
collection | PubMed |
description | Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2. |
format | Online Article Text |
id | pubmed-6031000 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-60310002018-07-10 CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures Kuriata, Aleksander Gierut, Aleksandra Maria Oleniecki, Tymoteusz Ciemny, Maciej Paweł Kolinski, Andrzej Kurcinski, Mateusz Kmiecik, Sebastian Nucleic Acids Res Web Server Issue Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2. Oxford University Press 2018-07-02 2018-05-14 /pmc/articles/PMC6031000/ /pubmed/29762700 http://dx.doi.org/10.1093/nar/gky356 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Web Server Issue Kuriata, Aleksander Gierut, Aleksandra Maria Oleniecki, Tymoteusz Ciemny, Maciej Paweł Kolinski, Andrzej Kurcinski, Mateusz Kmiecik, Sebastian CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures |
title | CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures |
title_full | CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures |
title_fullStr | CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures |
title_full_unstemmed | CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures |
title_short | CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures |
title_sort | cabs-flex 2.0: a web server for fast simulations of flexibility of protein structures |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031000/ https://www.ncbi.nlm.nih.gov/pubmed/29762700 http://dx.doi.org/10.1093/nar/gky356 |
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