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Proteins. 2005 Aug 1;60(2):269-74.

Docking essential dynamics eigenstructures.

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1
Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK.

Abstract

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.

PMID:
15981272
DOI:
10.1002/prot.20569
[Indexed for MEDLINE]
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