An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.
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.
Mazin
Pavel V
PV
Cellnetworks, University of Heidelberg, Heidelberg, Germany. olga.kalinina@bioquant.uni-heidelberg.de.
Gelfand
Mikhail S
MS
Mironov
Andrey A
AA
Rakhmaninova
Aleksandra B
AB
Rubinov
Anatoly R
AR
Russell
Robert B
RB
Kalinina
Olga V
OV