Protein-protein docking predictions for the CAPRI experiment

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2003-07, Vol.52 (1), p.118-122
• Main Authors: Gray, Jeffrey J., Moughon, Stewart E., Kortemme, Tanja, Schueler-Furman, Ora, Misura, Kira M.S., Morozov, Alexandre V., Baker, David
• Format: Article
• Language: English
• Subjects: Algorithms; alpha-Amylases - chemistry; alpha-Amylases - metabolism; Amino Acid Sequence; Antibodies - chemistry; Antibodies - immunology; Antigens, Viral; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; biomolecular free energy function; Capsid Proteins - chemistry; Capsid Proteins - immunology; Exotoxins - chemistry; Exotoxins - metabolism; flexible side chains; Hemagglutinin Glycoproteins, Influenza Virus - chemistry; Hemagglutinin Glycoproteins, Influenza Virus - immunology; high-resolution refinement; Macromolecular Substances; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Models, Molecular; Molecular Sequence Data; Monte Carlo Method; Phosphoenolpyruvate Sugar Phosphotransferase System - chemistry; Phosphoenolpyruvate Sugar Phosphotransferase System - metabolism; protein binding; Protein Interaction Mapping; protein interactions; Protein-Serine-Threonine Kinases - chemistry; Protein-Serine-Threonine Kinases - metabolism; Proteins - chemistry; Proteins - metabolism; Receptors, Antigen, T-Cell, alpha-beta - chemistry; Receptors, Antigen, T-Cell, alpha-beta - metabolism; Sequence Alignment
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.10384

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 refinement with side‐chain conformational changes and rigid body minimization. Decoys (∼106 per target) 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 experimental structure to 1.5 Å RMSD and included 48 of 65 correct residue–residue contacts. Target 7 was predicted 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 version of the protocol in round 1, target 1 was predicted 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. © 2003 Wiley‐Liss, Inc.