Eberhardt Jerome, Santos-Martins Diogo, Tillack Andreas F, Forli Stefano
Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, 92037 California, United States.
J Chem Inf Model. 2021 Aug 23;61(8):3891-3898. doi: 10.1021/acs.jcim.1c00203. Epub 2021 Jul 19.
AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks support for modeling specific features such as macrocycles or explicit water molecules. Here, we describe the implementation of this functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Furthermore, we implemented Python bindings to facilitate scripting and the development of docking workflows. This work is an effort toward the unification of the features of the AutoDock4 and AutoDock Vina programs. The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina.
AutoDock Vina可以说是用于分子对接的最快且使用最广泛的开源程序之一。然而，与AutoDock Suite中的其他程序相比，它缺乏对诸如大环或显式水分子等特定特征建模的支持。在此，我们描述了在AutoDock Vina 1.2.0中此功能的实现。此外，AutoDock Vina 1.2.0支持AutoDock4.2评分函数、多个配体的同时对接以及用于对接大量配体的批处理模式。此外，我们实现了Python绑定以促进脚本编写和对接工作流程的开发。这项工作是朝着统一AutoDock4和AutoDock Vina程序的功能所做的努力。源代码可在https://github.com/ccsb-scripps/AutoDock-Vina获取。
