Protein-protein docking predictions for the CAPRI experiment

Proteins. 2003 Jul 1;52(1):118-22. doi: 10.1002/prot.10384.

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 (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.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Antibodies / chemistry
  • Antibodies / immunology
  • Antigens, Viral*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Capsid Proteins / chemistry
  • Capsid Proteins / immunology
  • Exotoxins / chemistry
  • Exotoxins / metabolism
  • Hemagglutinin Glycoproteins, Influenza Virus / chemistry
  • Hemagglutinin Glycoproteins, Influenza Virus / immunology
  • 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 Interaction Mapping
  • 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
  • alpha-Amylases / chemistry
  • alpha-Amylases / metabolism

Substances

  • Antibodies
  • Antigens, Viral
  • Bacterial Proteins
  • Capsid Proteins
  • Exotoxins
  • Hemagglutinin Glycoproteins, Influenza Virus
  • Macromolecular Substances
  • Membrane Proteins
  • Proteins
  • Receptors, Antigen, T-Cell, alpha-beta
  • SpeA protein, Streptococcus pyogenes
  • VP6 protein, Rotavirus
  • Phosphoenolpyruvate Sugar Phosphotransferase System
  • phosphocarrier protein HPr
  • HPr kinase
  • Protein Serine-Threonine Kinases
  • alpha-Amylases

Associated data

  • PDB/1SBB