Bastard Karine, Saladin Adrien, Prévost Chantal
LABIS, Genoscope, CEA, 2 rue Gaston Cremieux, F-91057 Evry Cedex, France; E-Mail:
Int J Mol Sci. 2011 Feb 22;12(2):1316-33. doi: 10.3390/ijms12021316.
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.
理论方法和计算机计算资源的迅速发展，已使计算机模拟方法成为一种可想象的工具，能够从大分子组合的各个独立元件的结构出发，预测其三维结构。然而，某些类型的复合物对于大分子对接方法而言仍是一项真正的挑战。在这些复合物中，诸如环或结构域等蛋白质部分在结合时会发生大幅度变形，从而重塑与伴侣蛋白或DNA可接触的表面。我们讨论了对接方法中与处理此类重排相关的问题，并综述了目前正在探索的策略，以及它们的局限性和成功之处。
