Protein-protein docking predictions for the CAPRI experiment. Proteins: Struct Funct Genet

ABSTRACT We predicted structures for all seven targets in the CAPRI experiment using a new method in development at the time of the challenge. The technique includes a low-resolution rigid body Monte Carlo search followed by high-resolution re-finement with side-chain conformational changes and rigid body minimization. Decoys (106 per tar-get) were discriminated using a scoring function including van der Waals and solvation interactions, hydrogen bonding, residue–residue pair statistics, and rotamer probabilities. Decoys were ranked, clustered,manually inspected, and selected. The top ranked model for target 6 predicted the experimen-tal structure to 1.5 Å RMSD and included 48 of 65 correct residue–residue contacts. Target 7 was pre-dicted at 5.3 Å RMSD with 22 of 37 correct residue– residue contacts using a homology model from a known complex structure. Using a preliminary ver-sion of the protocol in round 1, target 1 was pre-dicted within 8.8 Å although few contacts were correct. For targets 2 and 3, the interface locations and a small fraction of the contacts were correctly identified. Proteins 2003;52:118–122. © 2003Wiley-Liss, Inc. Key words: protein binding; protein interactions; biomolecular free energy function; high-resolution refinement; flexible side chain