title: PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  The PiSQRD web server, which requires Java, is available free of charge for academic users at http://pisqrd.escience-lab.org.
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati and eLab, CNR-INFM Democritos Simulation Centre, via Beirut 2-4, 34151 Trieste and Italian Institute of Technology, Genoa, Italy.
authors.forename: T
authors.initials: T
authors.lastname: Aleksiev
authors.forename: R
authors.initials: R
authors.lastname: Potestio
authors.forename: F
authors.initials: F
authors.lastname: Pontiggia
authors.forename: S
authors.initials: S
authors.lastname: Cozzini
authors.forename: C
authors.initials: C
authors.lastname: Micheletti
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins