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Many protein families contain homologous proteins that have a
common biological function but different specificity. Given a
multiple sequence alignment of a family divided into specificity
groups, SDPpred predicts a set of alignment positions (SDP,
Specificity-Determining Positions) that determine differences in
the functional specificity. If analysing transmembrane proteins,
there is a possibility to predict TM segments first, and then use
special matrices for TM segments in the analysis. Additional
feature is SDP-profile based prediction of specificity.
The server implements the algorithm described in (when results are used, please site):
- Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB. (2004)
Automated selection of positions determining functional
specificity of proteins by comparative analysis of orthologous
groups in protein families. Protein Sci 13(2):
443-56. (PubMed)
This is SDPpred v.2. The first version can be found at http://monkey.belozersky.msu.ru/~psn/
and is described in
- Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB.
(2004)
SDPpred: a tool for prediction of amino acid residues that determine
differences in functional specificity of homologous proteins.
Nucleic Acids Res 32(Web Server issue):
W424-8. (PubMed)
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