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.
Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK.
Diana
D
Mustard
David W
DW
Ritchie
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D019281:Dimerization; D020407:Internet; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D040681:Structural Homology, Protein
D046911:Macromolecular Substances