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Keywords:

  • protein–protein interaction;
  • induced fit;
  • elastic network model;
  • docking minimization;
  • protein–protein complex formation

ABSTRACT

A coarse-grained (CG) protein model implemented in the ATTRACT protein–protein docking program has been employed to predict protein–protein complex structures in CAPRI Rounds 22–27. For six targets, acceptable or better quality solutions have been submitted corresponding to ∼60% of all targets. For one target, promising results on the prediction of the hydration structure at the protein–protein interface have been achieved. New approaches for the rapid flexible refinement have been developed based on a combination of atomistic representation of the bonded geometry and a CG description of nonbonded interactions. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed. Proteins 2013; 81:2167–2174. © 2013 Wiley Periodicals, Inc.