Protein domain interaction interface database: InterPare

Cited 45 time in scopus
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Title
Protein domain interaction interface database: InterPare
Author(s)
SungSam Gong; C Park; H Choi; J Ko; InSoo Jang; J Lee; D M Bolser; D Oh; D S Kim; Jong Bhak
Bibliographic Citation
BMC Bioinformatics, vol. 6, pp. 207-207
Publication Year
2005
Abstract
Background: Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently. Description: We introduce a large-scale protein domain interaction interface database called InterPare (http://interpare.net). It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. InterPare includes visualization tools to display protein interior, surface, and interaction interfaces. It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. The atom coordinates that belong to interface, surface, and interior regions can be downloaded from the website. Conclusion: InterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known. As of November 2004, there were 10,583 (Geometric distance), 10,431 (ASA), and 11,010 (Voronoi diagram) entries in the Protein Data Bank (PDB) containing interfaces, according to the above three methods. In the case of the geometric distance method, there are 31,620 inter-chain domain-domain interaction interfaces and 12,758 intra-chain domain-domain interfaces.
ISSN
1471-2105
Publisher
Springer-BMC
DOI
http://dx.doi.org/10.1186/1471-2105-6-207
Type
Article
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