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Article SwarmDock and the Use of Normal Modes in Protein-Protein

By Iain H. Moal and Paul A. Bates

Abstract

Abstract: Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking

Topics: elastic network model, normal mode analysis, particle swarm optimisation
Year: 2010
OAI identifier: oai:CiteSeerX.psu:10.1.1.292.6499
Provided by: CiteSeerX
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