Cited by 38,412Computational Drug Discovery MethodsAdvanced Chemical Physics StudiesProtein Structure and Dynamics

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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Trott, Oleg, Olson, Arthur J.·2010·Journal of Computational Chemistry

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Abstract

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed‐up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010

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Authors: Trott, O., & Olson, A. J.
Affiliations: Scripps Research Institute (US)
Corresponding author: Olson, Arthur J.
ORCID: Olson, Arthur J.
Venue: Journal of Computational Chemistry
Publisher: Wiley
Published: 2009-06-04
Volume: 31
Issue: 2
Pages: 455-461
ISSN: 0192-8651 (ISSN-L)
1096-987X
DOI: 10.1002/jcc.21334
PMC: PMC3041641
OpenAlex: W2134967712
Cited by: 38,412
References: 24
Citations by year: 2026: 4951 · 2025: 5289 · 2024: 4793 · 2023: 4241 · 2022: 4250 · 2021: 3687 · 2020: 2903 · 2019: 1858 · 2018: 1560 · 2017: 1225 · 2016: 1035 · 2015: 832 · 2014: 613 · 2013: 508 · 2012: 346
FWCI: 212.46
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Journal of Computational Chemistry (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institutes of Health
National Institute of General Medical Sciences (R01GM069832)
Topics: Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords: AutoDock Vina, molecular docking, virtual screening, scoring functions, binding mode prediction, multithreading, multi-core parallelization, grid map
MeSH terms: Algorithms, Automation, Binding Sites, Hydrogen Bonding, Ligands, Sensitivity and Specificity, Software, Solvents, Thermodynamics, Time Factors, Computational Biology, Molecular Dynamics Simulation, Hydrophobic and Hydrophilic Interactions

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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