Scoppi: a Structural Classification of Protein-protein Interfaces.
From: Biotechnological Centre of TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany.
Nucleic acids research
- Publish Date: Jan 2006
- ISSN: 1362-4962
- Volume: 34
- Issue: Database issue
- Pages: D310-4
- Medium: Internet
- Language: English
- Citation (JAMA): Winter Christof, Henschel Andreas, Kim Wan Kyu, et al. Scoppi: a Structural Classification of Protein-protein Interfaces.. Nucleic Acids Res. Jan 2006;34:D310-4
Abstract
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.
Mesh Headings (Keywords): Binding Sites, Cytokines, Databases, Protein, Gene Fusion, Internet, Models, Molecular, Protein Interaction Mapping, Protein Structure, Tertiary, Proteins, Sequence Alignment, Sequence Analysis, Protein, Trypsin, User-Computer Interface
Check for Full Text / PubMed Unique Identifier (PMID): 16381874
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