Abstract

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 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 programs. The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina

Keywords

AutoDockPython (programming language)Computer scienceDocking (animal)Source codeScripting languageProgramming languageOperating systemChemistry

MeSH Terms

AnimalsBoidaeLigandsMolecular Docking SimulationSoftware

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Publication Info

Year
2021
Type
article
Volume
61
Issue
8
Pages
3891-3898
Citations
5176
Access
Closed

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Cite This

Jérôme Eberhardt, Diogo Santos‐Martins, Andreas F. Tillack et al. (2021). AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling , 61 (8) , 3891-3898. https://doi.org/10.1021/acs.jcim.1c00203

Identifiers

DOI
10.1021/acs.jcim.1c00203
PMID
34278794
PMCID
PMC10683950

Data Quality

Data completeness: 90%