Protein-protein docking predictions for the CAPRI experiment

Jeffrey J. Gray*, Stewart E. Moughon, Tanja Kortemme, Ora Schueler-Furman, Kira Misura, Alexandre V. Morozov, David Baker

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

92 Scopus citations


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 residueresidue 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.

Original languageAmerican English
Pages (from-to)118-122
Number of pages5
JournalProteins: Structure, Function and Genetics
Issue number1
StatePublished - 1 Jul 2003
Externally publishedYes


  • Biomolecular free energy function
  • Flexible side chains
  • High-resolution refinement
  • Protein binding
  • Protein interactions


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