T. Aleksiev, R. Potestio, S. Cozzini and C. Micheletti
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
Bioinformatics 25 2743-2744 (2009)
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Motivation: The PiSQRD web resource can be used to subdivide protein structures in quasi-rigid dynamical domains. These domains are groups of amino acids that in the course of protein equilibrium fluctuations behave approximately as rigid bodies. The user provides as input the biomolecular structure, and specifies what fraction of protein internal fluctuation should be captured by the rigid body motion of the domains; the web server returns an interactive graphical representation of the optimal grouping of the amino acids in the number of domains satisfying the required mobility constraint.
Availability: The PiSQRD web server is available free of charge for academic users at the address: http://pisqrd.escience-lab.org . Interactive visualization of the results requires Java.