GWOVina 1.0 – Fast Protein-ligand Docking tool based on GWO and AutoDock Vina

GWOVina 1.0

:: DESCRIPTION

Based on the implementation of AutoDock Vina, GWOVina employs grey wolf optimization (GWO) algorithm to speed up the search for optimal ligand poses.

::DEVELOPER

Computational Biology and Bioinformatics Lab (CBBio)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

GWOVina

:: MORE INFORMATION

Citation

Wong KM, Tai HK, Siu SWI.
GWOVina: A grey wolf optimization approach to rigid and flexible receptor docking.
Chem Biol Drug Des. 2021 Jan;97(1):97-110. doi: 10.1111/cbdd.13764. Epub 2020 Aug 10. PMID: 32679606; PMCID: PMC7818481.

PSOVina 2.0 – Fast Protein-ligand Docking tool based on PSO and AutoDock Vina

PSOVina 2.0

:: DESCRIPTION

PSOVina combines the particle swarm optimization (PSO) algorithm with the efficient Broyden-Fletcher-Goldfarb-Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking.

::DEVELOPER

Computational Biology and Bioinformatics Lab (CBBio)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PSOVina

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2015 Jun;13(3):1541007. doi: 10.1142/S0219720015410073. Epub 2015 Feb 10.
PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking.
Ng MC, Fong S, Siu SW.

JADOPPT – Java based AutoDock Preparing and Processing Tool

JADOPPT

:: DESCRIPTION

JADOPPT is a tool for automatically preparing and processing multiple AutoDock results, thus allowing their simultaneous analysis and comparison.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux /MacOs
Java

:: DOWNLOAD

JADOPPT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):583-585. doi: 10.1093/bioinformatics/btw677.
JADOPPT: java based AutoDock preparing and processing tool.
García-Pérez C, Peláez R, Therón R, Luis López-Pérez J.

AutoDock 4.2.6 / AutoDockTools 1.5.6 – Suite of Automated Docking Tools

AutoDock 4.2.6

:: DESCRIPTION

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

AutoDockTools (ADT) is graphical front-end for setting up and running AutoDock – an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

::DEVELOPER

Molecular Graphics Laboratory , The Scripps Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

AutoDock , AutoDockTools

:: MORE INFORMATION

Citation

Morris,G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009)
Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity.
J.Comput.Chem. 2009 Dec;30(16):2785-91.