Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

International Journal of Molecular Sciences

Karine Bastard²  Adrien Saladin¹ 

[1] MTI, INSERM UMR-M 973, Paris Diderot-Paris 7 University, Bât Lamarck, 35 rue Hélène Brion, F-75205 Paris Cedex 13, France; E-Mail:;LABIS, Genoscope, CEA, 2 rue Gaston Cremieux, F-91057 Evry Cedex, France; E-Mail:

关键词: macromolecular docking;    flexibility;    protein loops and domains;   

DOI  :  10.3390/ijms12021316

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2011 by the authors; licensee MDPI, Basel, Switzerland.