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Bioinformatics Advance Access published online on August 20, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp512
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains

T. Aleksiev 1, R. Potestio 1,*, F. Pontiggia 1, S. Cozzini 1,2 and C. Micheletti 1,2

1Scuola Internazionale Superiore di Studi Avanzati and eLab, via Beirut 2-4, 34151 Trieste, Italy
2CNR-INFM Democritos Simulation Centre, via Beirut 2-4, 34151 Trieste, Italy

*To whom correspondence should be addressed. Raffaello Potestio, E-mail: potestio{at}sissa.it


  Abstract

Summary: The PiSQRD web resource can be used to subdivide protein structures in quasi-rigid dynamical domains. The latter are groups of amino acids behaving as approximately-rigid units in the course of protein equilibrium fluctuations. The PiSQRD server takes as input a biomolecular structure and the desired fraction of protein internal fluctuations that must be accounted for by the relative rigidbody motion of the dynamical domains. Next, the lowest-energy modes of fluctuation of the protein (optionally provided by the user) are calculated and used to identify the rigid subunits. The resulting optimal subdivision is returned through a web page containing both interactive graphics and detailed data output.

Availability: The PiSQRD web server, which requires Java, is available free of charge for academic users at the address: http://pisqrd.escience-lab.org.

Contact: potestio{at}sissa.it

Associate Editor: Prof. Burkhard Rost

Received on June 17, 2009; revised on August 10, 2009; accepted on August 16, 2009

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