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PIBASE: a comprehensive database of structurally defined protein interfaces.

Fred P Davis1, Andrej Sali

  • 1Graduate Group in Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, 94143, USA.

Bioinformatics (Oxford, England)
|January 20, 2005
PubMed
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PIBASE is a new database of protein-protein interactions derived from the Protein Data Bank (PDB). It categorizes interfaces and binding sites, aiding structural biology research.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) has grown significantly, necessitating better organization of protein-protein interaction data.
  • High-resolution structural data requires effective tools for analysis and utilization.

Purpose of the Study:

  • To develop PIBASE, a comprehensive relational database of structurally defined protein-domain interfaces.
  • To maximize the utility of protein-protein interaction data within the PDB.

Main Methods:

  • Extracted binary interfaces from PDB and Probable Quaternary Structure server using domain assignments from CATH and SCOP.
  • Calculated geometric, physiochemical, and topological properties for complexes, domains, interfaces, and binding sites.
  • Filtered for distinct domain-domain interfaces and classified complexes and interfaces based on topology.

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Main Results:

  • PIBASE contains 158,915 interacting domain pairs from 105,061 domains across 2125 SCOP families.
  • Identified 20,912 distinct domain-domain interfaces after redundancy reduction.
  • Classified complexes into 989 topological classes and interfaces/binding sites into 18,755 and 30,975 topological classes, respectively.

Conclusions:

  • PIBASE provides a valuable resource for studying protein-protein interactions.
  • The database's topological classifications facilitate deeper structural and functional analysis.
  • Demonstrated utility through various current applications.