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Int. J. Mol. Sci. 2011, 12(2), 1316-1333; doi:10.3390/ijms12021316

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

1 LABIS, Genoscope, CEA, 2 rue Gaston Cremieux, F-91057 Evry Cedex, France 2 MTI, INSERM UMR-S 973, Paris Diderot-Paris 7 University, Bât Lamarck, 35 rue Hélène Brion, F-75205 Paris Cedex 13, France 3 LBT-UPR 9080 CNRS, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris, France
* Author to whom correspondence should be addressed.
Received: 10 December 2010 / Revised: 7 January 2011 / Accepted: 8 February 2011 / Published: 22 February 2011
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA.We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.
Keywords: macromolecular docking; flexibility; protein loops and domains macromolecular docking; flexibility; protein loops and domains
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Bastard, K.; Saladin, A.; Prévost, C. Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking. Int. J. Mol. Sci. 2011, 12, 1316-1333.

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