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Nucleic Acids Research 2006 34(Database Issue):D310-D314; doi:10.1093/nar/gkj099
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Nucleic Acids Research, 2006, Vol. 34, Database issue D310-D314
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

SCOPPI: a structural classification of protein–protein interfaces

Christof Winter1, Andreas Henschel1, Wan Kyu Kim1 and Michael Schroeder1,*

1Biotechnological Centre of TU Dresden Tatzberg 47-51, 01307 Dresden, Germany

*To whom correspondence should be addressed. Tel: +49 351 463 40062; Fax: +49 351 463 40061; Email: ms{at}biotec.tu-dresden.de

Received August 15, 2005. Revised October 17, 2005. Accepted October 17, 2005.

SCOPPI, the structural classification of protein–protein interfaces, is a comprehensive database that classifies and annotates domain interactions derived from all known protein structures. SCOPPI applies SCOP domain definitions and a distance criterion to determine inter-domain interfaces. Using a novel method based on multiple sequence and structural alignments of SCOP families, SCOPPI presents a comprehensive geometrical classification of domain interfaces. Various interface characteristics such as number, type and position of interacting amino acids, conservation, interface size, and permanent or transient nature of the interaction are further provided. Proteins in SCOPPI are annotated with Gene Ontology terms, and the ontology can be used to quickly browse SCOPPI. Screenshots are available for every interface and its participating domains. Here, we describe contents and features of the web-based user interface as well as the underlying methods used to generate SCOPPI's data. In addition, we present a number of examples where SCOPPI becomes a useful tool to analyze viral mimicry of human interface binding sites, gene fusion events, conservation of interface residues and diversity of interface localizations. SCOPPI is available at http://www.scoppi.org.


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