蛋白质-蛋白质分子对接中打分函数研究进展

分子对接是研究分子间相互作用与识别的有效方法.其中,用于近天然构象挑选的打分函数的合理设计对于对接中复合物结构的成功预测至关重要.本文回顾了蛋白质-蛋白质分子对接组合打分函数中一些主要打分项,包括几何互补项、界面接触面积、范德华相互作用能、静电相互作用能以及统计成对偏好势等打分项的计算方法.结合本研究小组的工作,介绍了目前普遍使用的打分方案以及利用与结合位点有关的信息进行结构筛选的几种策略,比较并总结了常用打分函数的特点.最后,分析并指出了当前蛋白质-蛋白质对接打分函数所存在的主要问题,并对未来的工作进行了展望.

Progress in the Scoring Functions of Protein-Protein Docking

Molecular docking technology is an effective approach for prediction of intermolecular interactions and recognition. The design of a scoring function for selecting near-native structures is very important for successful prediction of complex structures. In this article, the main computational methods for scoring items in protein-protein docking, such as geometric complementarity, contact area, van der Waals’ interaction, electrostatic interaction, and statistical pair propensity potential, are reviewed. Including our work, we introduce commonly used scoring schemes and some strategies in screening decoys based on the information for protein binding sites. The characteristic scoring functions in the commonly used docking programs are compared and summarized. The major problems in the existing scoring function in protein-protein docking are discussed along with prospect for future research.