Research Article

Protein–protein docking predictions for the CAPRI experiment

  1. Jeffrey J. Gray*,
  2. Stewart E. Moughon,
  3. Tanja Kortemme,
  4. Ora Schueler-Furman,
  5. Kira M.S. Misura,
  6. Alexandre V. Morozov,
  7. David Baker

Article first published online: 14 MAY 2003

DOI: 10.1002/prot.10384

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Special Issue: CAPRI—Critical Assessment of PRedicted Interactions

Volume 52, Issue 1, pages 118–122, 1 July 2003

Additional Information

How to Cite

Gray, J. J., Moughon, S. E., Kortemme, T., Schueler-Furman, O., Misura, K. M., Morozov, A. V. and Baker, D. (2003), Protein–protein docking predictions for the CAPRI experiment. Proteins: Structure, Function, and Bioinformatics, 52: 118–122. doi: 10.1002/prot.10384

Author Information

  1. Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington

*Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles, Baltimore, MD 21218

Publication History

  1. Issue published online: 14 MAY 2003
  2. Article first published online: 14 MAY 2003
  3. Manuscript Accepted: 12 NOV 2002
  4. Manuscript Received: 30 OCT 2002

Funded by

  • National Institutes of Health K01 Mentored Quantitative Research Fellowship in Genomics
  • European Molecular Biology Organization
  • Human Frontier Science Program Organization. Grant Number: LT00358/2000-M
  • Helen Hay Whitney Foundation
  • Damon-Runyon Fellowship, Damon Runyon Cancer Research Foundation. Grant Number: DRG-1704-02
  • National Institutes of Health

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Keywords:

  • protein binding;
  • protein interactions;
  • biomolecular free energy function;
  • high-resolution refinement;
  • flexible side chains

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 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.

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