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Bioinformatics Advance Access originally published online on May 7, 2009
Bioinformatics 2009 25(13):1709-1710; doi:10.1093/bioinformatics/btp304
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FlexServ: an integrated tool for the analysis of protein flexibility

Jordi Camps 1,2, Oliver Carrillo 1, Agustí Emperador 1, Laura Orellana 1, Adam Hospital 1,3, Manuel Rueda 1, Damjan Cicin-Sain 1,3, Marco D'Abramo 1,4, Josep Lluís Gelpí 1,2,4,* and Modesto Orozco 1,3,4,*

1Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona 08028 and Barcelona Supercomputing Centre, 2National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 31, Barcelona 08034, Spain, 3National Institute of Bioinformatics, Structural Bioinformatics, Josep Samitier 1-5 and 4Department of Biochemistry and Molecular Biology, University of Barcelona, Av Diagonal 645, Barcelona 08028, Spain

*To whom correspondence should be addressed.


  Abstract

Summary: FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. The server allows a complete analysis of flexibility using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemann's indexes, residue correlation, chain-correlations, dynamic domain determination, hinge point detections, etc. Data is presented through a web interface as plain text, 2D and 3D graphics.

Availability: http://mmb.pcb.ub.es/FlexServ; http://www.inab.org

Contact: modesto{at}mmb.pcb.ub.es or gelpi{at}mmb.pcb.ub.es

Supplementary information: Additional information and methodology details can be found at http://mmb.pcb.ub.es/FlexServ/help.

Associate Editor: Thomas Lengauer

Received on December 28, 2008; revised on April 23, 2009; accepted on May 4, 2009

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