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

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 implementati...

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Bibliographic Details
Published inJournal of chemical information and modeling Vol. 61; no. 8; pp. 3891 - 3898
Main Authors Eberhardt, Jerome, Santos-Martins, Diogo, Tillack, Andreas F, Forli, Stefano
Format Journal Article
LanguageEnglish
Published Washington American Chemical Society 23.08.2021
Subjects
Computational Chemistry
Ligands
Molecular docking
Source code
Source programs
Water chemistry
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Summary: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.
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These authors contributed equally to this work.
ISSN:1549-9596
1549-960X
1549-960X
DOI:10.1021/acs.jcim.1c00203