ABOUT P-cats:

The catalytic or functionally important residues of a protein are known to exist in evolutionarily constrained regions. However, the patterns of residue conservation alone are sometimes not very informative, depending on the homologous sequences available for a given query protein. Here, we present an integrated method, named P-cats, to locate the catalytic residues in a protein from its sequence and structure. Mutations of functional residues usually decrease the activity, but concurrently often increase in stability. Also, catalytic residues tend to occupy partially buried sites in holes or clefts on the molecular surface. P-cats takes all of these analyses, i.e., the stability profile and surface geometry, into account as well as sequence conservation. A user, who would like to ask the location of catalytic, or functionally important residues to P-cats, should only prepare the coordinate of query structure in PDB format. It will take some time to make an analysis so the result will be sent by E-mail.

REFERENCE: Ota M., Kinoshita K. and Nishikawa K. (2003) Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J. Mol. Biol. 327, 1053-1064
PMID: 12662930 [PubMed - indexed for MEDLINE]

 

SUBMISSION:

1. Upload your query structure in PDB format:
2. Enter your E-mail address:
3. Enter the e-value for the homologous sequence search by BLAST: 0.01 10E-5 10E-10 10E-20 10E-30 10E-50 10E-100
4. Select the sequence database: swissprot refseq nr
5. Submit to P-cats ! or Reset
6. .. and Analyse the P-cats's reply in the return mail

If you have any question or suggestion, please do not hesitate to contact us!
mail: p-cats@tsurumi.yokohama-cu.ac.jp

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M. Ota & K. Kinishota, May 2003