Protein-protein docking predictions for the CAPRI experiment.
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 (approximately 10(6) 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 A RMSD and included 48 of 65 correct residue-residue contacts. Target 7 was predicted at 5.3 A 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 A although few contacts were correct. For targets 2 and 3, the interface locations and a small fraction of the contacts were correctly identified.
Gray
Jeffrey J
JJ
Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington, USA.
Moughon
Stewart E
SE
Kortemme
Tanja
T
Schueler-Furman
Ora
O
Misura
Kira M S
KM
Morozov
Alexandre V
AV
Baker
David
D
D000465:Algorithms; D000595:Amino Acid Sequence; D000906:Antibodies / Q000737:chemistry / Q000276:immunology; D000956:Antigens, Viral; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry / Q000276:immunology; D005098:Exotoxins / Q000737:chemistry / Q000378:metabolism; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry / Q000276:immunology; D046911:Macromolecular Substances; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry / Q000378:metabolism; D025941:Protein Interaction Mapping; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D000516:alpha-Amylases / Q000737:chemistry / Q000378:metabolism
D000906:Antibodies; D000956:Antigens, Viral; D001426:Bacterial Proteins; D036022:Capsid Proteins; D005098:Exotoxins; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D046911:Macromolecular Substances; D008565:Membrane Proteins; D011506:Proteins; D016693:Receptors, Antigen, T-Cell, alpha-beta; C117980:SpeA protein, Streptococcus pyogenes; C061332:VP6 protein, Rotavirus; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases; D000516:alpha-Amylases