Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function

Proteins. 2005 Aug 1;60(2):314-8. doi: 10.1002/prot.20576.

Abstract

We entered the CAPRI experiment during the middle of Round 4 and have submitted predictions for all 6 targets released since then. We used the following procedures for docking prediction: (1) the identification of possible binding region(s) of a target based on known biological information, (2) rigid-body sampling around the binding region(s) by using the docking program ZDOCK, (3) ranking of the sampled complex conformations by employing the DFIRE-based statistical energy function, (4) clustering based on pairwise root-mean-square distance and the DFIRE energy, and (5) manual inspection and relaxation of the side-chain conformations of the top-ranked structures by geometric constraint. Reasonable predictions were made for 4 of the 6 targets. The best fraction of native contacts within the top 10 models are 89.1% for Target 12, 54.3% for Target 13, 29.3% for Target 14, and 94.1% for Target 18. The origin of successes and failures is discussed. .

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Animals
  • Binding Sites
  • Computational Biology / methods*
  • Computer Simulation
  • Databases, Protein
  • Dimerization
  • Macromolecular Substances
  • Models, Molecular
  • Models, Statistical
  • Molecular Conformation
  • Protein Binding*
  • Protein Conformation
  • Protein Folding
  • Protein Interaction Mapping / methods*
  • Protein Structure, Tertiary
  • Proteomics / methods*
  • Reproducibility of Results
  • Sequence Alignment
  • Software
  • Structural Homology, Protein

Substances

  • Macromolecular Substances