Docking essential dynamics eigenstructures

Proteins. 2005 Aug 1;60(2):269-74. doi: 10.1002/prot.20569.


This article describes our attempts to dock the targets in CAPRI Rounds 3-5 using Hex 4.2, and it introduces a novel essential dynamics approach to generate multiple feasible conformations for docking. In the blind trial, the basic Hex algorithm found 1 high-accuracy solution for CAPRI Target 12, and several further medium- and low-accuracy solutions for Targets 11, 12, 13, and 14. Subsequent a posteriori docking of the targets using essential dynamics "eigenstructures" was found to give consistently better predictions than rigidly docking only the unbound or model-built starting structures. Some suggestions to improve this promising new approach are presented.

Publication types

  • Research Support, Non-U.S. Gov't

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 Binding*
  • Protein Conformation
  • Protein Folding
  • Protein Interaction Mapping / methods*
  • Protein Structure, Tertiary
  • Proteomics / methods*
  • Reproducibility of Results
  • Software
  • Structural Homology, Protein


  • Macromolecular Substances