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Protocols

AutoDock specifications

Information


Unique identifier OMICS_19997
Name AutoDock
Alternative names Autodock4, AutoDockTools4, AutoDockTools, ADT
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 4.2.6
Stability Stable
Source code URL http://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/autodocksuite-4.2.6-src.tar.gz
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/AutoDock

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Versioning


No version available

Documentation


Maintainer


  • person_outline Arthur J. Olson

Additional information


http://mgl.scripps.edu/forum/viewforum.php?f=8&sid=4ae9c72b889354bbb4ede2340fd4622f5bNE,L5d

Publications for AutoDock

AutoDock citations

 (1741)
library_books

A new insight into identification of in silico analysis of natural compounds targeting GPR120

2018
PMCID: 5951878
PMID: 29780684
DOI: 10.1007/s13721-018-0166-0

[…] inspiration. Among the 100 lead molecules, 89 molecules were selected based on the criteria of satisfying Lipinski’s rule of five with zero violations. All docking calculations were carried out using AutoDock 4.0/ADT and the dlg files generated were analyzed for their binding conformations. Analysis was based on free energy of binding, lowest docked energy, and calculated RMSD values (Table ). The […]

library_books

Computer aided design of amino acid based therapeutics: a review

2018
Drug Des Devel Ther
PMCID: 5958949
DOI: 10.2147/DDDT.S159767

[…] get-based peptide design, two remarkable methodologies including the VitAL method and an approach developed by Bhattacherjee and Wallin were introduced. The VitAL method pools verterbi algorithm with AutoDock to design peptides for the binding sites of a target. The “Bhattacherjee and Wallin” approach explores both peptide sequence and conformational space around a protein target at the same time. […]

library_books

In vitro and in silico studies of terpenes, terpenoids and related compounds with larvicidal and pupaecidal activity against Culex quinquefasciatus Say (Diptera: Culicidae)

2018
Chem Cent J
PMCID: 5945571
PMID: 29748726
DOI: 10.1186/s13065-018-0425-2

[…] protein of Aedes aegypti (PDB: 1PZ4) [] reported in the RCSB Protein Data Bank. The final model was subjected to Ramachandran analysis using the Rampage server []. Docking analysis was done using the AutoDock4 software []. For the docking the active site was defined considering the residues within a grid of 60 A° × 60 A° × 60 A° centered in the active site, with an initial population of 100 random […]

library_books

Insight into resistance mechanism of anaplastic lymphoma kinase to alectinib and JH VIII 157 02 caused by G1202R solvent front mutation

2018
Drug Des Devel Ther
PMCID: 5953303
PMID: 29785088
DOI: 10.2147/DDDT.S147104

[…] h predicts the preferred orientation of one molecule to another – was used to construct the ALKG1202R/alectinib, ALKWT/JH-VIII-157-02, and ALKG1202R/JH-VIII-157-02 models by the latest version of the AutoDock 4.2.6 package. AutoDock is a flexible docking program, which is one of the most cited docking software in the research community. It is especially effective for protein–ligand docking. Prior […]

library_books

Discovery of small molecules through pharmacophore modeling, docking and molecular dynamics simulation against Plasmodium vivax Vivapain 3 (VP 3)

2018
PMCID: 5944417
PMID: 29756074
DOI: 10.1016/j.heliyon.2018.e00612

[…] To construe the hopeful ligands for inhibitors of VP-3, all the primary hits were docked into the newly recognized binding pocket of VP-3 by the AutoDock 4.2 in PyRx virtual screening Tool. The docking simulation energies was determined for each legend with 10 exhaustiveness. Active site grid dimensions were set as X = 64.3194, Y = 42.7549 and […]

call_split

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

[…] hich a succession of steps consisting of a mutation and a local optimization are taken, with each step being accepted according to the Metropolis criterion. In the present study, we have utilized the AutoDock plugin that can be incorporated in PyMOL, to analyze the binding sites and prepare the input parameters for AutoDock Vina runs. The grid for blind docking runs was generated based on the avai […]

Citations

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AutoDock institution(s)
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA; Department of Cognitive Science, University of California at San Diego, La Jolla, CA, USA
AutoDock funding source(s)
Supported under grant RO1 GM069832 from the National Institutes of Health

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