Dockground resource for studying protein-protein interfaces

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 30, 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. © 2006 Oxford University Press.