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

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 interfa...

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Main Authors:	Paul A. Bates, Iain H. Moal
Format:	Article
Language:	English
Published:	MDPI AG 2010-09-01
Series:	International Journal of Molecular Sciences
Subjects:	elastic network model normal mode analysis particle swarm optimisation PSO protein flexibility RTB CAPRI
Online Access:	http://www.mdpi.com/1422-0067/11/10/3623/

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spelling	doaj-00a0cd393b8e4f55ab4327bf17b418b52020-11-25T02:43:58ZengMDPI AGInternational Journal of Molecular Sciences1422-00672010-09-0111103623364810.3390/ijms11103623SwarmDock and the Use of Normal Modes in Protein-Protein DockingPaul A. BatesIain H. MoalHere 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. http://www.mdpi.com/1422-0067/11/10/3623/elastic network modelnormal mode analysisparticle swarm optimisationPSOprotein flexibilityRTBCAPRI
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Paul A. Bates Iain H. Moal
spellingShingle	Paul A. Bates Iain H. Moal SwarmDock and the Use of Normal Modes in Protein-Protein Docking International Journal of Molecular Sciences elastic network model normal mode analysis particle swarm optimisation PSO protein flexibility RTB CAPRI
author_facet	Paul A. Bates Iain H. Moal
author_sort	Paul A. Bates
title	SwarmDock and the Use of Normal Modes in Protein-Protein Docking
title_short	SwarmDock and the Use of Normal Modes in Protein-Protein Docking
title_full	SwarmDock and the Use of Normal Modes in Protein-Protein Docking
title_fullStr	SwarmDock and the Use of Normal Modes in Protein-Protein Docking
title_full_unstemmed	SwarmDock and the Use of Normal Modes in Protein-Protein Docking
title_sort	swarmdock and the use of normal modes in protein-protein docking
publisher	MDPI AG
series	International Journal of Molecular Sciences
issn	1422-0067
publishDate	2010-09-01
description	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.
topic	elastic network model normal mode analysis particle swarm optimisation PSO protein flexibility RTB CAPRI
url	http://www.mdpi.com/1422-0067/11/10/3623/
work_keys_str_mv	AT paulabates swarmdockandtheuseofnormalmodesinproteinproteindocking AT iainhmoal swarmdockandtheuseofnormalmodesinproteinproteindocking
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SwarmDock and the Use of Normal Modes in Protein-Protein Docking

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