Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI

Proteins. 2005 Aug 1;60(2):263-8. doi: 10.1002/prot.20568.

Abstract

We have submitted models for all 9 targets in Rounds 3-5 of CAPRI and have predicted at least 30% of the correct contacts for 4 of the targets and at least 10% of the correct contacts for another 4 targets. We have employed a variety of techniques but have had the greatest success by combining established rigid-body docking with a variety of initial conformations generated by molecular dynamics.

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Computer Simulation
  • Crystallography, X-Ray
  • Databases, Protein
  • Dimerization
  • Internet
  • Macromolecular Substances
  • Models, Molecular
  • Models, Statistical
  • Molecular Conformation
  • Mutation
  • Protein Conformation
  • Protein Folding
  • Protein Interaction Mapping / methods*
  • Protein Structure, Tertiary
  • Proteomics / methods*
  • Reproducibility of Results
  • Software
  • Static Electricity
  • Structural Homology, Protein

Substances

  • Macromolecular Substances