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WEBnm@ v2.0: Web server and services for comparing protein flexibility

BACKGROUND: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics–function relationship can be gained by comparing protein motions between p...

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Autores principales: Tiwari, Sandhya P, Fuglebakk, Edvin, Hollup, Siv M, Skjærven, Lars, Cragnolini, Tristan, Grindhaug, Svenn H, Tekle, Kidane M, Reuter, Nathalie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339738/
https://www.ncbi.nlm.nih.gov/pubmed/25547242
http://dx.doi.org/10.1186/s12859-014-0427-6
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author Tiwari, Sandhya P
Fuglebakk, Edvin
Hollup, Siv M
Skjærven, Lars
Cragnolini, Tristan
Grindhaug, Svenn H
Tekle, Kidane M
Reuter, Nathalie
author_facet Tiwari, Sandhya P
Fuglebakk, Edvin
Hollup, Siv M
Skjærven, Lars
Cragnolini, Tristan
Grindhaug, Svenn H
Tekle, Kidane M
Reuter, Nathalie
author_sort Tiwari, Sandhya P
collection PubMed
description BACKGROUND: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics–function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. RESULTS: We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma. CONCLUSION: WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0427-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-43397382015-02-26 WEBnm@ v2.0: Web server and services for comparing protein flexibility Tiwari, Sandhya P Fuglebakk, Edvin Hollup, Siv M Skjærven, Lars Cragnolini, Tristan Grindhaug, Svenn H Tekle, Kidane M Reuter, Nathalie BMC Bioinformatics Software BACKGROUND: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics–function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. RESULTS: We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma. CONCLUSION: WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0427-6) contains supplementary material, which is available to authorized users. BioMed Central 2014-12-30 /pmc/articles/PMC4339738/ /pubmed/25547242 http://dx.doi.org/10.1186/s12859-014-0427-6 Text en © Tiwari et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Tiwari, Sandhya P
Fuglebakk, Edvin
Hollup, Siv M
Skjærven, Lars
Cragnolini, Tristan
Grindhaug, Svenn H
Tekle, Kidane M
Reuter, Nathalie
WEBnm@ v2.0: Web server and services for comparing protein flexibility
title WEBnm@ v2.0: Web server and services for comparing protein flexibility
title_full WEBnm@ v2.0: Web server and services for comparing protein flexibility
title_fullStr WEBnm@ v2.0: Web server and services for comparing protein flexibility
title_full_unstemmed WEBnm@ v2.0: Web server and services for comparing protein flexibility
title_short WEBnm@ v2.0: Web server and services for comparing protein flexibility
title_sort webnm@ v2.0: web server and services for comparing protein flexibility
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339738/
https://www.ncbi.nlm.nih.gov/pubmed/25547242
http://dx.doi.org/10.1186/s12859-014-0427-6
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