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Keywords:

  • protein–protein interactions;
  • protein–protein docking;
  • CAPRI;
  • rigid-body cross-docking;
  • molecular dynamics

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. Proteins 2005;60:263–268. © 2005 Wiley-Liss, Inc.