A new optimization model of molecular docking is proposed, and a fast flexible docking method based on an improved adaptive genetic algorithm is developed in this paper. The algorithm takes some advanced techniques, such as multi-population genetic strategy, entropy-based searching technique with self-adaptation and the quasi-exact penalty. A new iteration scheme in conjunction with above techniques is employed to speed up the optimization process and to ensure very rapid and steady convergence. The docking accuracy and efficiency of the method are evaluated by docking results from GOLD test data set, which contains 134 protein-ligand complexes. In over 66.2% of the complexes, the docked pose was within 2.0 A root-mean-square deviation (RMSD) of the X-ray structure. Docking time is approximately in proportion to the number of the rotatable bonds of ligands.

译文

提出了一种新的分子对接优化模型,提出了一种基于改进的自适应遗传算法的快速柔性对接方法。该算法采用了一些先进的技术,例如多种群遗传策略,具有自适应的基于熵的搜索技术和准精确惩罚。结合上述技术,采用了新的迭代方案来加快优化过程并确保非常快速和稳定的收敛。通过来自包含134蛋白质-配体复合物的GOLD测试数据集的对接结果来评估该方法的对接精度和效率。在超过66.2% 的复合体中,对接的姿势在x射线结构的均方根偏差 (RMSD) 2.0内。对接时间与配体的可旋转键的数量大致成比例。

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