Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Kuriata, Aleksander, Gierut, Aleksandra Maria, Oleniecki, Tymoteusz, Ciemny, Maciej Paweł, Kolinski, Andrzej, Kurcinski, Mateusz, Kmiecik, Sebastian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
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
_version_ 1783337235240714240
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
work_keys_str_mv AT kuriataaleksander cabsflex20awebserverforfastsimulationsofflexibilityofproteinstructures
AT gierutaleksandramaria cabsflex20awebserverforfastsimulationsofflexibilityofproteinstructures
AT olenieckitymoteusz cabsflex20awebserverforfastsimulationsofflexibilityofproteinstructures
AT ciemnymaciejpaweł cabsflex20awebserverforfastsimulationsofflexibilityofproteinstructures
AT kolinskiandrzej cabsflex20awebserverforfastsimulationsofflexibilityofproteinstructures
AT kurcinskimateusz cabsflex20awebserverforfastsimulationsofflexibilityofproteinstructures
AT kmieciksebastian cabsflex20awebserverforfastsimulationsofflexibilityofproteinstructures