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Bioinformatics Advance Access published online on May 7, 2009
Bioinformatics, 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. Spain and Barcelona Supercomputing Centre, Jordi Girona 31, Barcelona 08034, Spain.
2National Institute of Bioinformatics, Computational Bioinformatics, Jordi Girona 31, Barcelona 08034, Spain.
3National Institute of Bioinformatics, Structural Bioinformatics, Josep Samitier 1-5, Barcelona 08028, Spain.
4Department of Biochemistry and Molecular Biology, University of Barcelona, Av Diagonal 645, Barcelona 08028, Spain.

*To whom correspondence should be addressed. Dr. Josep Gelpi, E-mail: gelpi{at}bq.ub.es


  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: Prof. Thomas Lengauer

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

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