Bonvin Alexandre M J J
Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, NL-3584 CH, Utrecht, The Netherlands.
Curr Opin Struct Biol. 2006 Apr;16(2):194-200. doi: 10.1016/j.sbi.2006.02.002. Epub 2006 Feb 17.
Predicting the structure of protein-protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes. Flexibility can be addressed at several levels: implicitly, by smoothing the protein surfaces or allowing some degree of interpenetration (soft docking) or by performing multiple docking runs from various conformations (cross or ensemble docking); or explicitly, by allowing sidechain and/or backbone flexibility. Although significant improvements have been achieved in the modeling of sidechains, methods for the explicit inclusion of backbone flexibility in docking are still being developed. A few novel approaches have emerged involving collective degrees of motion, multicopy representations and multibody docking, which should allow larger conformational changes to be modeled.
使用对接方法预测蛋白质-蛋白质复合物的结构是一个难题，其主要挑战包括识别正确的解决方案，以及妥善处理分子柔性和构象变化。柔性可以在几个层面上解决：隐式地，通过平滑蛋白质表面或允许一定程度的相互穿透（软对接），或者从各种构象进行多次对接运行（交叉或整体对接）；或者显式地，通过允许侧链和/或主链柔性。尽管在侧链建模方面已经取得了显著进展，但对接中显式纳入主链柔性的方法仍在开发中。已经出现了一些涉及集体运动自由度、多拷贝表示和多体对接的新方法，这些方法应该能够对更大的构象变化进行建模。
