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

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

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)
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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

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MDPI and ACS Style

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.

AMA Style

Moal IH, Bates PA. SwarmDock and the Use of Normal Modes in Protein-Protein Docking. International Journal of Molecular Sciences. 2010; 11(10):3623-3648.

Chicago/Turabian Style

Moal, Iain H.; Bates, Paul A. 2010. "SwarmDock and the Use of Normal Modes in Protein-Protein Docking." Int. J. Mol. Sci. 11, no. 10: 3623-3648.

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