SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins
1 Department of Bioengineering and Bioinformatics, Moscow State University, Vorob'evy gory, 1-73, Moscow, 119992, Russia, 2 State Scintific Center GosNIIGenetika, 1st Dorozhny pr., 1, Moscow, 113545, Russia and 3 Institute for Problems of Information Transmission RAS, Bolshoi Karetny per., 19, Moscow, 127994, Russia
* To whom correspondence should be addressed. Tel: +7 095 9394331; Fax: +7 095 2090579; Email: abr{at}belozersky.msu.ru
Received February 12, 2004; Revised and Accepted March 24, 2004
SDPpred (Specificity Determining Position prediction) is a tool for prediction of residues in protein sequences that determine the proteins' functional specificity. It is designed for analysis of protein families whose members have biochemically similar but not identical interaction partners (e.g. different substrates for a family of transporters). SDPpred predicts residues that could be responsible for the proteins' choice of their correct interaction partners. The input of SDPpred is a multiple alignment of a protein family divided into a number of specificity groups, within which the interaction partner is believed to be the same. SDPpred does not require information about the secondary or three-dimensional structure of proteins. It produces a set of the alignment positions (specificity determining positions) that determine differences in functional specificity. SDPpred is available at http://math.genebee.msu.ru/~psn/.
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