Classification of protein complexes based on docking difficulty

Proteins. 2005 Aug 1;60(2):176-80. doi: 10.1002/prot.20554.

Abstract

Based on the results of several groups using different docking methods, the key properties that determine the expected success rate in protein-protein docking calculations are measures of conformational change, interface area, and hydrophobicity. A classification of protein complexes in terms of these measures provides a prediction of docking difficulty. This classification is used to study the targets of the CAPRI docking experiment. Results show that targets with a moderate expected difficulty were indeed predicted well by a number of groups, whereas the use of additional a priori information was necessary to obtain good results for some very difficult targets. The analysis indicates that CAPRI and other relatively large-scale docking studies represent very important steps toward understanding the capabilities and limitations of current protein-protein docking methods.

Publication types

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

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Computer Simulation
  • Databases, Protein
  • Dimerization
  • Internet
  • Macromolecular Substances
  • Models, Molecular
  • Models, Statistical
  • Molecular Conformation
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping / methods*
  • Proteins / chemistry*
  • Proteins / classification
  • Proteomics / methods*
  • Reproducibility of Results
  • Software
  • Structural Homology, Protein

Substances

  • Macromolecular Substances
  • Proteins