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Related Experiment Videos

A protein domain interaction interface database: InterPare.

Sungsam Gong1, Changbum Park, Hansol Choi

  • 1National Genome Information Center, KRIBB, Daejeon, Korea. ssgong@kaist.ac.kr

BMC Bioinformatics
|August 27, 2005
PubMed
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InterPare is a new database that catalogs protein interaction interfaces, aiding drug discovery. It uses geometric, ASA, and Voronoi methods to identify and visualize these crucial protein sites.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein interactions are vital for cellular function and are evolutionarily conserved.
  • Identifying interaction sites is key for rational drug discovery and understanding cellular disorders.
  • Large-scale classification of protein interfaces can accelerate the discovery of new drug targets.

Purpose of the Study:

  • To introduce InterPare, a comprehensive database of protein domain interaction interfaces.
  • To provide researchers with a resource for identifying and analyzing protein interaction sites.
  • To facilitate efficient drug target discovery through large-scale interface data.

Main Methods:

  • InterPare utilizes geometric distance, Accessible Surface Area (ASA), and Voronoi diagram methods to detect interfaces.

Related Experiment Videos

  • The database includes both inter-chain and intra-chain interfaces.
  • Visualization tools and statistical analyses of amino acid propensities are provided.

    • Main Results:

    • InterPare contains large-scale interface data for proteins with known 3D structures.
    • As of November 2004, thousands of PDB entries were processed using the three detection methods.
    • Significant numbers of inter-chain (31,620) and intra-chain (12,758) domain-domain interfaces were identified using the geometric distance method.

    Conclusions:

    • InterPare is an open, public database server for protein interaction interface information.
    • The database offers extensive data on protein interfaces, supporting structural biology and drug discovery research.
    • It provides downloadable atom coordinates for interface, surface, and interior regions.