title: ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces.
abstract: BACKGROUND
  Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the interface formed by protein-protein association would allow us to better understand protein interaction networks on one hand, and to design molecules that can engage a given interface and thereby control protein function on the other hand.
  
  
  RESULTS
  ProFace is a suite of programs that uses a file, containing atomic coordinates of a multi-chain molecule, as input and analyzes the interface between any two or more subunits. The interface residues are shown segregated into spatial patches (if such a clustering is possible based on an input threshold distance) and/or core and rim regions. A number of physicochemical parameters defining the interface is tabulated. Among the different output files, one contains the list of interacting residues across the interface. Results can be used to infer if a particular interface belongs to a homodimeric molecule.
  
  
  CONCLUSIONS
  A web-server, ProFace (available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html) has been developed for dissecting protein-protein interfaces and deriving various physicochemical parameters.
authors.affiliation: Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India. rudra@bic.boseinst.ernet.in
authors.forename: Rudra P
authors.initials: RP
authors.lastname: Saha
authors.forename: Ranjit P
authors.initials: RP
authors.lastname: Bahadur
authors.forename: Arumay
authors.initials: A
authors.lastname: Pal
authors.forename: Saptarshi
authors.initials: S
authors.lastname: Mandal
authors.forename: Pinak
authors.initials: P
authors.lastname: Chakrabarti
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D019295:Computational Biology; D017868:Cyclic AMP-Dependent Protein Kinases / Q000737:chemistry* / Q000378:metabolism*; D019281:Dimerization; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012984:Software; D012985:Software Design
chemical_list: D017868:Cyclic AMP-Dependent Protein Kinases