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Jérôme Eberhardt, Diogo Santos‐Martins, Andreas F. Tillack, Stefano Forli
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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Eberhardt, J., Santos‐Martins, D., Tillack, A. F., & Forli, S. (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
Eberhardt, Jérôme, et al. "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings." Journal of Chemical Information and Modeling, vol. 61, no. 8, 2021, pp. 3891–3898, https://doi.org/10.1021/acs.jcim.1c00203.
Eberhardt, Jérôme, Diogo Santos‐Martins, Andreas F. Tillack, and Stefano Forli. "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings." Journal of Chemical Information and Modeling 61, no. 8 (2021): 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203.
Eberhardt J., Santos‐Martins D., Tillack A. F. [и др.] AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings // Journal of Chemical Information and Modeling. — 2021. — Vol. 61, № 8. — P. 3891–3898. — URL: https://doi.org/10.1021/acs.jcim.1c00203
@article{eberhardt2021autodock,
title = {{AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings}},
author = {Jérôme Eberhardt and Diogo Santos‐Martins and Andreas F. Tillack and Stefano Forli},
journal = {Journal of Chemical Information and Modeling},
year = {2021},
volume = {61},
number = {8},
pages = {3891--3898},
doi = {10.1021/acs.jcim.1c00203},
url = {https://doi.org/10.1021/acs.jcim.1c00203}
}TY - JOUR AU - Eberhardt, Jérôme AU - Santos‐Martins, Diogo AU - Tillack, Andreas F. AU - Forli, Stefano TI - AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings JO - Journal of Chemical Information and Modeling VL - 61 IS - 8 SP - 3891 EP - 3898 PY - 2021 DA - 2021/07/19 DO - 10.1021/acs.jcim.1c00203 UR - https://doi.org/10.1021/acs.jcim.1c00203 ER -
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