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Functionally and structurally relevant residues in PROSITE motif descriptors

Part 3. Proteomics

3.6. Proteome Families

Short Specialist Review

  1. Christian J. A. Sigrist,
  2. Edouard De Castro,
  3. Petra S. Langendijk-Genevaux,
  4. Virginie Le Saux,
  5. Amos Bairoch,
  6. Nicolas Hulo

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g306318

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Sigrist, C. J. A., De Castro, E., Langendijk-Genevaux, P. S., Saux, V. L., Bairoch, A. and Hulo, N. 2005. Functionally and structurally relevant residues in PROSITE motif descriptors. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6:84.

Author Information

  1. University of Geneva, Geneva, Switzerland

Publication History

  1. Published Online: 15 APR 2005

Abstract

PROSITE is an annotated collection of motif descriptors, which are either patterns (regular expressions) or generalized profiles (weight matrices). Whereas patterns perform well for the identification of short well-conserved regions such as active sites, profiles usually cover the full length of the protein or domain and can accept a mismatch at a highly conserved position if the rest of the sequence shows a sufficiently high level of similarity. Hence, a profile can match a structural domain even if the active site is mutated and thus is no longer functional. To distinguish these cases and make functional predictions more accurate, biologically meaningful residues of a profile can be tagged and the corresponding residues in the sequence retrieved and checked for their biological properties.

Keywords:

  • domain;
  • signature database;
  • motif descriptor;
  • profile;
  • functional prediction