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. 2004 Jul 1;32(Web Server issue):W424-8.
doi: 10.1093/nar/gkh391.

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins

Olga V Kalinina  1 , Pavel S Novichkov, Andrey A Mironov, Mikhail S Gelfand, Aleksandra B Rakhmaninova
Affiliations

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins

Olga V Kalinina et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
Residues making ‘structural clasps’ in the structure of the tetramer of the GlpF of Escherichia coli (1fx8, biological subunit). SDPs lying on the surface of contact between subunits are shown by white spheres.
Figure 2
Figure 2
A typical SDPpred query.
Figure 3
Figure 3
SDPpred output: (A) alignment of the query protein family with SDPs highlighted; (B) detailed description of the SDPs; (C) probability plot.
See this image and copyright information in PMC

References

    1. Lichtarge O., Bourne,H,R. and Cohen,F,E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342–358. - PubMed
    1. Johnson J.M. and Church,G.M. (2000) Predicting ligand-binding function in families of bacterial receptors. Proc. Natl Acad. Sci. USA, 97, 3965–3970. - PMC - PubMed
    1. Livingstone C. and Barton,G. (1993). Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9, 745–756. - PubMed
    1. Casari G., Sander,C. and Valencia,A. (1995). A method to predict functional residues in proteins. Nat. Struct. Biol., 2, 171–178. - PubMed
    1. Gaucher E.A., Gu,X., Miyamoto,M.M. and Benner,S.A. (2002). Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem. Sci., 27, 315–321. - PubMed