Nucleic Acids Research Advance Access originally published online on October 25, 2009
Nucleic Acids Research 2010 38(Database issue):D161-D166; doi:10.1093/nar/gkp885
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Nucleic Acids Research, 2010, Vol. 38, Database issue D161-D166
© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
PROSITE, a protein domain database for functional characterization and annotation
1Swiss Institute of Bioinformatics (SIB), Centre Médical Universitaire and 2Structural Biology and Bioinformatics Department, University of Geneva, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland
*To whom correspondence should be addressed. Tel: +41 22 379 58 68; Fax: +41 22 379 58 58; Email: christian.sigrist{at}isb-sib.ch
Received September 3, 2009. Revised October 2, 2009. Accepted October 2, 2009.
PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 (
70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/.