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

Overview of attention for article published in BMC Bioinformatics, December 2014
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Title
WEBnm@ v2.0: Web server and services for comparing protein flexibility
Published in
BMC Bioinformatics, December 2014
DOI 10.1186/s12859-014-0427-6
Pubmed ID
Authors

Sandhya P Tiwari, Edvin Fuglebakk, Siv M Hollup, Lars Skjærven, Tristan Cragnolini, Svenn H Grindhaug, Kidane M Tekle, Nathalie Reuter

Abstract

BackgroundNormal 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.ResultsWe 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.ConclusionWEBnm@ 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.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 74 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Norway 2 3%
Poland 1 1%
United States 1 1%
Canada 1 1%
Unknown 69 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 19 26%
Researcher 17 23%
Student > Bachelor 10 14%
Student > Master 9 12%
Professor 6 8%
Other 9 12%
Unknown 4 5%
Readers by discipline Count As %
Agricultural and Biological Sciences 24 32%
Biochemistry, Genetics and Molecular Biology 19 26%
Chemistry 7 9%
Computer Science 4 5%
Engineering 2 3%
Other 9 12%
Unknown 9 12%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 31 December 2014.
All research outputs
#3,799,220
of 4,691,823 outputs
Outputs from BMC Bioinformatics
#2,517
of 2,706 outputs
Outputs of similar age
#121,897
of 155,197 outputs
Outputs of similar age from BMC Bioinformatics
#145
of 150 outputs
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