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)
Link to full text.
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
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.