An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.

Algorithms for Molecular Biology : AMB
Pavel V MazinOlga V Kalinina

Abstract

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. 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. SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.

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Citations

May 31, 2012·Nucleic Acids Research·Timothy PadawerDegeng Wang
Jun 13, 2012·Nucleic Acids Research·Abhijit ChakrabortySaikat Chakrabarti
May 31, 2013·Journal of the Royal Society, Interface·Briana J Dunn, Chaitan Khosla
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May 13, 2020·Journal of Viral Hepatitis·Julia DietzUNKNOWN European HCV Resistance Study Group
Nov 11, 2020·The Journal of Biological Chemistry·Melissa J RuggieroBruno Hagenbuch

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Software Mentioned

SDPgroup
SDPclust
SDPsite
FASS
MB
Trace Suite
SDPlight
Protein Keys
SDPpred
method

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