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


Algorithm in details



What is SDPpred?

Input format

Output format


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. More information about what we mean by this and about SDPpred in general you can find here.

The server implements the algorithm described in:
  • 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)
See also:
  • Mirny LA, Gelfand MS. (2002) Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 321: 7-20. (PubMed)
A detailed description of the algorithm you can find here.

We plan to to implement also the algorithm that predicts specificity for those members of the family, whose specificity is unknown.

If you have a correctly formatted alignment, click here or follow the "Go!" link.

To find out about input alignment format click here or follow the "Input format" link. To find out about what you get as a result click here or follow the "Output format" link. To see an example of how all this works click here or follow the "Example" link.

If you have questions or comments, please contact us.
Version 1.0

This is the first release of the program. If you observe a bug or suspicious behavior, or get a nonsense result, please send us a note, containing the query alignment and the parameters you've used. Thank you.