Docking essential dynamics eigenstructures

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. (c) 2005 Wiley-Liss, Inc.