The binding pose and affinity between a ligand and enzyme are very important pieces of information for computer-aided drug design. In the initial stage of a drug discovery project, this information is often obtained by using molecular docking methods. Autodock4 and Autodock Vina are two commonly used open-source and free software tools to perform this task, and each has been cited more than 6000 times in the last ten years. It is of great interest to compare the success rate of the two docking software programs for a large and diverse set of protein-ligand complexes. In this study, we selected 800 protein-ligand complexes for which both PDB structures and experimental binding affinity are available. Docking calculations were performed for these complexes using both Autodock4 and Autodock Vina with different docking options related to computing resource consumption and accuracy. Our calculation results are in good agreement with a previous study that the Vina approach converges much faster than AD4 one. However, interestingly, AD4 shows a better performance than Vina over 21 considered targets, whereas the Vina protocol is better than the AD4 package for 10 other targets. There are 16 complexes for which both the AD4 and Vina protocols fail to produce a reasonable correlation with respected experiments so both are not suitable to use to estimate binding free energies for these cases. In addition, the best docking option for performing the AD4 approach is the long option. However, the short option is the best solution for carrying out Vina docking. The obtained results probably will be useful for future docking studies in deciding which program to use.

中文翻译：

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Autodock Vina采用更精确的绑定姿势，但Autodock4形成更好的绑定亲和力。

配体与酶之间的结合姿势和亲和力是计算机辅助药物设计中非常重要的信息。在药物开发项目的初始阶段，通常通过使用分子对接方法来获得此信息。Autodock4和Autodock Vina是执行此任务的两个常用的开源和免费软件工具，在过去十年中，每个工具都被引用了6000多次。比较两个对接软件程序对大量多样的蛋白质-配体复合物的成功率非常感兴趣。在这项研究中，我们选择了800种蛋白质-配体复合物，其PDB结构和实验结合亲和力均可用。使用Autodock4和Autodock Vina对这些复合体执行了对接计算，并具有与计算资源消耗和准确性有关的不同对接选项。我们的计算结果与先前的研究（Vina方法的收敛速度比AD4方法的收敛速度快得多）非常吻合。但是，有趣的是，在考虑的21个目标上，AD4的性能比Vina更好，而对于其他10个目标，Vina协议的性能优于AD4程序包。对于AD16和Vina协议，有16种复合物无法与相关实验产生合理的相关性，因此这两种复合物都不适合用于估计这些情况下的结合自由能。此外，执行AD4方法的最佳对接选项是长选项。然而，简短的选择是进行Vina对接的最佳解决方案。获得的结果可能对将来决定使用哪个程序的对接研究有用。