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Int. J. Mol. Sci. 2010, 11(10), 3623-3648; doi:10.3390/ijms11103623
Article

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

 and *
Received: 2 July 2010 / Revised: 29 July 2010 / Accepted: 16 September 2010 / Published: 28 September 2010
(This article belongs to the Special Issue Advances in Molecular Recognition)
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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.
Keywords: elastic network model; normal mode analysis; particle swarm optimisation; PSO; protein flexibility; RTB; CAPRI elastic network model; normal mode analysis; particle swarm optimisation; PSO; protein flexibility; RTB; CAPRI
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Moal, I.H.; Bates, P.A. SwarmDock and the Use of Normal Modes in Protein-Protein Docking. Int. J. Mol. Sci. 2010, 11, 3623-3648.

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