Journal Article

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

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

in Bioinformatics

Volume 25, issue 20, pages 2743-2744
Published in print October 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI:
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains

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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 rigid-body 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


Journal Article.  1410 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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