Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Motivation: A number of proteins of known three-dimensional (3D) structure exist, with yet unknown function. In light of the recent progress in structure determination methodology, this number is likely to increase rapidly. A novel method is presented here: ‘Rate4Site’, which maps the rate of evolution among homologous proteins onto the molecular surface of one of the homologues whose 3D-structure is known. Functionally important regions often correspond to surface patches of slowly evolving residues. Results: Rate4Site estimates the rate of evolution of amino acid sites using the maximum likelihood (ML) principle. The ML estimate of the rates considers the topology and branch lengths of the phylogenetic tree, as well as the underlying stochastic process. To demonstrate its potency, we study the Src SH2 domain. Like previously established methods, Rate4Site detected the SH2 peptide-binding groove. Interestingly, it also detected inter-domain interactions between the SH2 domain and the rest of the Src protein that other methods failed to detect. Availability: Rate4Site can be downloaded at: http://ashtoret.tau.ac.il/ It is implemented as a web server at: bioinfo.tau.ac.il/ConSurf

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References in zbMATH (referenced in 7 articles )

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  1. Carbone, A.; Dib, L.: Co-evolution and information signals in biological sequences (2011)
  2. Guharoy, Mainak; Chakrabarti, Pinak: Conserved residue clusters at protein-protein interfaces and their use in binding site identification (2010) ioport
  3. Liu, Qian; Li, Jinyan: Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective (2010) ioport
  4. Kalinina, Olga V.; Gelfand, Mikhail S.; Russell, Robert B.: Combining specificity determining and conserved residues improves functional site prediction (2009) ioport
  5. Livesay, Dennis R.; Kidd, Patrick D.; Eskandari, Sepehr; Roshan, Usman: Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na^+ symporter family (2007) ioport
  6. Mihalek, I.; Res, I.; Lichtarge, O.: Background frequencies for residue variability estimates: BLOSUM revisited (2007) ioport
  7. Tobi, Dror; Bahar, Ivet: Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? (2007) ioport