1. An automated stochastic approach to theidentification of the protein specificitydeterminants and functional subfamilies.
- Author
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Mazin, Pavel V., Gelfand, Mikhail S., Mironov, Andrey A., Rakhmaninova, Aleksandra B., Rubinov, Anatoly R., Russell, Robert B., and Kalinina, Olga V.
- Subjects
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COMPUTER software , *AMINO acid sequence - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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