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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

Iain H. Moal and Paul A. Bates*

Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY, UK

* Author to whom correspondence should be addressed.

Received: 2 July 2010; in revised form: 29 July 2010 / Accepted: 16 September 2010 / Published: 28 September 2010

(This article belongs to the Special Issue Advances in Molecular Recognition)

Download PDF Full-Text [1919 KB, uploaded 28 September 2010 11:48 CEST]

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

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