title: An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.
abstract: BACKGROUND
  Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.
  
  
  RESULTS
  We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server http://bioinf.fbb.msu.ru/SDPfoxWeb/ and a stand-alone Java application available from the website.
  
  
  CONCLUSIONS
  SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.
authors.affiliation: Cellnetworks, University of Heidelberg, Heidelberg, Germany. olga.kalinina@bioquant.uni-heidelberg.de.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Mazin
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Mironov
authors.forename: Aleksandra B
authors.initials: AB
authors.lastname: Rakhmaninova
authors.forename: Anatoly R
authors.initials: AR
authors.lastname: Rubinov
authors.forename: Robert B
authors.initials: RB
authors.lastname: Russell
authors.forename: Olga V
authors.initials: OV
authors.lastname: Kalinina