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

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

1
, 2
 and 3,*
Received: 10 December 2010; in revised form: 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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Abstract: 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 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

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.

AMA Style

Bastard K, Saladin A, Prévost C. Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking. International Journal of Molecular Sciences. 2011; 12(2):1316-1333.

Chicago/Turabian Style

Bastard, Karine; Saladin, Adrien; Prévost, Chantal. 2011. "Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking." Int. J. Mol. Sci. 12, no. 2: 1316-1333.



Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert