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.

SUBMITTER: Mazin PV 

PROVIDER: S-EPMC2914642 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature