title: In silico identification of functional regions in proteins.
abstract: BACKGROUND
  In silico prediction of functional regions on protein surfaces, i.e. sites of interaction with DNA, ligands, substrates and other proteins, is of utmost importance in various applications in the emerging fields of proteomics and structural genomics. When a sufficient number of homologs is found, powerful prediction schemes can be based on the observation that evolutionarily conserved regions are often functionally important, typically, only the principal functionally important region of the protein is detected, while secondary functional regions with weaker conservation signals are overlooked. Moreover, it is challenging to unambiguously identify the boundaries of the functional regions.
  
  
  METHODS
  We present a new methodology, called PatchFinder, that automatically identifies patches of conserved residues that are located in close proximity to each other on the protein surface. PatchFinder is based on the following steps: (1) Assignment of conservation scores to each amino acid position on the protein surface. (2) Assignment of a score to each putative patch, based on its likelihood to be functionally important. The patch of maximum likelihood is considered to be the main functionally important region, and the search is continued for non-overlapping patches of secondary importance.
  
  
  RESULTS
  We examined the accuracy of the method using the IGPS enzyme, the SH2 domain and a benchmark set of 112 proteins. These examples demonstrated that PatchFinder is capable of identifying both the main and secondary functional patches.
  
  
  BACKGROUND
  The PatchFinder program is available at: http://ashtoret.tau.ac.il/~nimrodg/
authors.affiliation: Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University Ramat Aviv 69978, Israel.
authors.forename: Guy
authors.initials: G
authors.lastname: Nimrod
authors.forename: Fabian
authors.initials: F
authors.lastname: Glaser
authors.forename: David
authors.initials: D
authors.lastname: Steinberg
authors.forename: Nir
authors.initials: N
authors.lastname: Ben-Tal
authors.forename: Tal
authors.initials: T
authors.lastname: Pupko
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry; D019143:Evolution, Molecular; D006801:Humans; D016013:Likelihood Functions; D008958:Models, Molecular; D015233:Models, Statistical; D011381:Programming Languages; D011487:Protein Conformation; D040901:Proteomics / Q000379:methods*; D012984:Software; D018909:src Homology Domains
chemical_list: D004247:DNA