AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

• DOI: 10.1021/acs.jcim.1c00203
• Publication Date: 2021-07-19T12:00:36Z
• Authors: Jerome Eberhardt; Diogo Santos-Martins; Andreas F. Tillack; Stefano Forli
• Keywords: source code; Information Systems not elsewhere classified; Biophysics; Ligands; Biochemistry; 03 medical and health sciences; open-source programs; Space Science; batch mode; AutoDock Vina programs; Genetics; Animals; Molecular Biology; Cancer; Pharmacology; docking workflows; 0303 health sciences; water molecules; AutoDock 4; Python bindings; Computational Biology; AutoDock Vina 1.2.0; AutoDock 4.2; AutoDock Suite; Python Bindings AutoDock Vina; Molecular Docking Simulation; Boidae; Force Field; Software; Neuroscience; Biological Sciences not elsewhere classified

AutoDock Vina is arguably one of the fastest and most widely used open-source docking engines. However, compared to other docking engines in the AutoDock Suite, it lacks features that support modeling of specific systems such as macrocycles or modeling water explicitly. Here, we describe the implementation of these 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 docking engines. The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina