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Bioinformatics Advance Access published online on August 23, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl447
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© 2006 The Author(s)
Received May 5, 2006
Revised July 29, 2006
Accepted August 16, 2006

Article

DOCKGROUND resource for studying protein-protein interfaces

Dominique Douguet 1 *, Huei-Chi Chen 2, Andrey Tovchigrechko 3, and Ilya A. Vakser 4

1 Centre de Biochimie Structurale (CNRS UMR 5048, INSERM UMR U554, UMI), 29, rue de Navacelles, 34090 Montpellier, France
2 Department of Applied Mathematics and Statistics, Math Tower 2-109, SUNY Stony Brook, Stony Brook, NY 11794-3600, USA
3 Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047-1620, USA
4 Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047-1620, USA; Department of Molecular Biosciences, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047-1620, USA

* To whom correspondence should be addressed.
Dominique Douguet, E-mail: douguet{at}cbs.cnrs.fr


  Abstract

Motivation: Public resources for studying protein interfaces are necessary for better understanding of molecular recognition and developing intermolecular potentials, search procedures, and scoring functions for the prediction of protein complexes.

Results: The first release of the DOCKGROUND resource implements a comprehensive database of co-crystallized (bound-bound) protein-protein complexes, providing foundation for the upcoming expansion to unbound (experimental and simulated) protein-protein complexes, modeled protein-protein complexes, and systematic sets of docking decoys. The bound-bound part of DOCKGROUND is a relational database of annotated structures based on the Biological Unit file (Biounit) provided by the RCSB as a separated file containing probable biological molecule. DOCKGROUND is automatically updated to reflect the growth of PDB. It contains 67,220 pairwise complexes that rely on 14,913 Biounit entries from 34,778 PDB entries (January 30th 2006). The database includes a dynamic generation of non-redundant datasets of pairwise complexes based either on the structural similarity (SCOP classification) or on user-defined sequence identity. The growing DOCKGROUND resource is designed to become a comprehensive public environment for developing and validating new methodologies for modeling of protein interactions.

Availability: DOCKGROUND is available at http://dockground.bioinformatics.ku.edu. The current first release implements the bound-bound part.

Associate Editor: Anna Tramontano
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