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PubMed · 15981272

Docking essential dynamics eigenstructures.

Diana Mustard·David W Ritchie
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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.

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AlgorithmsComputational BiologyComputer SimulationCrystallography, X-RayDatabases, ProteinDimerizationInternetMacromolecular SubstancesModels, MolecularModels, StatisticalMolecular ConformationMutationProtein BindingProtein ConformationProtein FoldingProtein Interaction MappingProtein Structure, TertiaryProteomicsReproducibility of ResultsSoftwareStructural Homology, ProteinJournal ArticleResearch Support, Non-U.S. Gov't

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Diana Mustard, David W Ritchie. 2005-08-01. Docking essential dynamics eigenstructures.. https://doi.org/10.1002/prot.20569

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