AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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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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Docking riboflavin, biotin, thiamine, and folate into the MMSYN1_0877 binding pocket produced X-SCORE affinities of −8.40, −6.77, −7.78, and −8.09 kcal/mol, respectively.
“each of four different vitamins (riboflavin, biotin, thiamine, and folate) were docked into the binding pocket of MMSYN1_0877.”
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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
- 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
- Locations
- Journal of Computational Chemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM069832)
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › 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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