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AutoDock Vina specifications

Information


Unique identifier OMICS_03790
Name AutoDock Vina
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0
Computer skills Advanced
Version 1.1.2
Stability Stable
Source code URL http://vina.scripps.edu/download/autodock_vina_1_1_2.tgz
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline AutoDock Vi

Additional information


Manual: http://vina.scripps.edu/manual.html

Publication for AutoDock Vina

AutoDock Vina citations

 (729)
library_books

Structural basis for the recognition of complex type N glycans by Endoglycosidase S

2018
Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] and the Man9GlcNAc product were modeled using GLYCAM-Web website (Complex Carbohydrate Research Center, University of Georgia, Athens, GA (http://www.glycam.com)). Ligand docking was performed using AutoDock Vina employing standard parameters. […]

library_books

Identification of new EphA4 inhibitors by virtual screening of FDA approved drugs

2018
Sci Rep
PMCID: 5943255
PMID: 29743517
DOI: 10.1038/s41598-018-25790-1

[…] We performed virtual screening for EphA4 inhibitor candidates using AutoDock Vina, a docking program that computationally examines the binding energy of a compound to its target. We ranked 1317 FDA-approved drugs according to their simulated binding energy. Based on a […]

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Nitrothiophene carboxamides, a novel narrow spectrum antibacterial series: Mechanism of action and Efficacy

2018
Sci Rep
PMCID: 5940854
PMID: 29740005
DOI: 10.1038/s41598-018-25407-7
call_split See protocol

[…] Blind docking experiments were performed for the hit molecule (compound 7) by Autodock Vina 1.1. The minocycline bound EcAcrB crystal structure (PDB ID: 4DX5) was considered for these experiments. AutoDock Vina 1.1, is an open-source program for docking simulations. It uses the […]

library_books

Defining a conformational ensemble that directs activation of PPARγ

2018
Nat Commun
PMCID: 5935666
PMID: 29728618
DOI: 10.1038/s41467-018-04176-x

[…] which is bound to PPARγ LBD in the 1FM9 crystal structure. GI262570 is identical to GW1929 for about 2/3 of the molecule. GW1929 was docked into the 1FM9 crystal structure with GI262570 removed using AutoDock Vina. The best scoring docked binding mode overlaid well with GI262570. In this docked model in the helix 12-interacting region, the two ligands themselves are identical. RESP charges for GW1 […]

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Residues contributing to drug transport by ABCG2 are localised to multiple drug binding pockets

2018
PMCID: 5934980
PMID: 29661915
DOI: 10.1042/BCJ20170923
call_split See protocol

[…] toDockTools (v1.5.6). A grid box centred on the approximate geometric midpoint of the TMD of an ABCG2 monomer (residues 517/518) with dimensions 36 × 20 × 20 (Å) was assigned as the search region for AutoDock Vina ([], The Scripps Research Institute) molecular docking software. The exhaustiveness of the search was manually set to 128, all other parameters being the default, to find the most energe […]

library_books

Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex

2018
PLoS One
PMCID: 5929560
PMID: 29715320
DOI: 10.1371/journal.pone.0196651

[…] To reveal the binding affinity and investigate the interaction between flavonoids and CDK6/cyclin D, a docking operation was performed using AutoDock Vina program[]. The software, which employs rapid gradient-optimization conformational search[] to locate the most suitable binding site[], can use all the rotatable bonds of the ligands to o […]

Citations

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AutoDock Vina institution(s)
The Scripps Research Institute, Molecular Biology, La Jolla, CA, USA
AutoDock Vina funding source(s)
This work was supported by the NIH grant 2R01GM069832.

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