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Open Access Database

A protein domain interaction interface database: InterPare

Sungsam Gong12, Changbum Park3, Hansol Choi2, Junsu Ko7, Insoo Jang1, Jungsul Lee4, Dan M Bolser5, Donghoon Oh7, Deok-Soo Kim6 and Jong Bhak18*

  • * Corresponding author: Jong Bhak j@bio.cc

Author Affiliations

1 National Genome Information Center (NGIC), KRIBB, Daejeon, Korea

2 Biomatics Lab, Dept. of BioSystems, KAIST, Daejeon, Korea

3 Geometric Computing Lab, Division of Computer Science, KAIST, Daejeon, Korea

4 Laboratory of Computational and Cellular Biology, Dept. of BioSystems, KAIST, Daejeon, Korea

5 MRC-DUNN, Cambridge, UK

6 Hanyang University, Seoul, Korea

7 Object Interaction Technologies, Inc., Daejeon, Korea

8 BiO center, Daejeon, Korea

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BMC Bioinformatics 2005, 6:207  doi:10.1186/1471-2105-6-207

Published: 25 August 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 webcite. 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.