蛋白质-配体分子对接中构象搜索方法

分子对接是研究蛋白质-配体分子间相互作用与识别的有效方法。分子间的相互作用过程中形成的近天然构象是结合自由能极低的构象，快速且准确搜索能量极低的构象对于蛋白质-配体分子对接至关重要。本文回顾了蛋白质-配体分子对接中主要的构象搜索算法，包括快速穷举搜索、启发式搜索和其他搜索方法，并列举了采用不同搜索算法的代表性分子对接软件。其次，介绍了蛋白质-配体分子对接的国际评估实验、常用的测试标准库和评价的重要指标。最后，分析并指出了当前蛋白质-配体对接构象搜索方法所存在的主要问题，并对未来的工作进行了展望。

Review of Conformational Searching Method for Protein-Ligand Molecular Docking

Molecular docking technology is an effective approach to protein-ligand interactions and recognition. The near-native conformations generated in the interaction process are the lowest energy conformations, so it is pivotal for the protein-ligand docking to searching these conformations quickly and accurately. Here we reviewed the main conformational searching methods in protein-ligand docking, including the exhaustive searching, heuristic searching and other searching strategies. Meanwhile, we listed the representative docking programs by using these different searching strategies. Furthermore, we introduced the international assessment of predicted interaction, the widely used testing benchmark and the evaluation indexes in protein-ligand docking. Finally, we pointed out the existing major problems of the search strategies in protein-ligand docking and gave a prospect for such field in the near future.