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Bioinformatics Advance Access originally published online on January 18, 2005
Bioinformatics 2005 21(9):1901-1907; doi:10.1093/bioinformatics/bti277
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

PIBASE: a comprehensive database of structurally defined protein interfaces

Fred P. Davis 1,2,3 and Andrej Sali 2,3,*

1Graduate Group in Biophysics, California Institute for Quantitative Biomedical Research, University of California San Francisco, CA 94143, USA
2Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California San Francisco, CA 94143, USA
3Department of Pharmaceutical Chemistry, California Institute for Quantitative Biomedical Research, University of California San Francisco, CA 94143, USA

*To whom correspondence should be addressed.

Motivation: In recent years, the Protein Data Bank (PDB) has experienced rapid growth. To maximize the utility of the high resolution protein–protein interaction data stored in the PDB, we have developed PIBASE, a comprehensive relational database of structurally defined interfaces between pairs of protein domains. It is composed of binary interfaces extracted from structures in the PDB and the Probable Quaternary Structure server using domain assignments from the Structural Classification of Proteins and CATH fold classification systems.

Results: PIBASE currently contains 158 915 interacting domain pairs between 105 061 domains from 2125 SCOP families. A diverse set of geometric, physiochemical and topologic properties are calculated for each complex, its domains, interfaces and binding sites. A subset of the interface properties are used to remove interface redundancy within PDB entries, resulting in 20 912 distinct domain–domain interfaces. The complexes are grouped into 989 topological classes based on their patterns of domain–domain contacts. The binary interfaces and their corresponding binding sites are categorized into 18 755 and 30 975 topological classes, respectively, based on the topology of secondary structure elements. The utility of the database is illustrated by outlining several current applications.

Availability: The database is accessible via the world wide web at http://salilab.org/pibase

Contact: sali{at}salilab.org

Supplementary information: http://salilab.org/pibase/suppinfo.html


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