Tag: AutoDock Vina

AutoGrow 4.0.3 – Use AutoDock Vina in Protein Inhibitor Design

AutoGrow 4.0.3

:: DESCRIPTION

AutoGrow (Java DOCK), uses fragment-based growing, docking, and evolutionary techniques.Due in part to the increasing availability of crystallographic protein structures as well as rapid improvements in computer power, the past few decades have seen an explosion in the field of computer-based rational drug design. Several algorithms have been developed to identify or generate potential ligands in silico by optimizing the ligand-receptor hydrogen bond, electrostatic, and hydrophobic interactions.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 AutoGrow

:: MORE INFORMATION

Citation

J Mol Graph Model, 44, 104-12 Jul 2013
AutoGrow 3.0: An Improved Algorithm for Chemically Tractable, Semi-Automated Protein Inhibitor Design
Jacob D Durrant , Steffen Lindert, J Andrew McCammon

Durrant, J. D.; Amaro, R. E.; McCammon, J. A. 2009.
AutoGrow: A Novel Algorithm for Protein Inhibitor Design
Chemical Biology & Drug Design. 73(2):168-78.

PaDEL-ADV 1.6 – Facilitate Virtual Screening with AutoDock Vina

PaDEL-ADV 1.6

:: DESCRIPTION

PaDEL-ADV is a software to perform virtual screening using AutoDock Vina.

::DEVELOPER

PaDEL-ADV team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PaDEL-ADV

:: MORE INFORMATION

Autodock/Vina plugin for PyMOL

Autodock/Vina plugin for PyMOL

:: DESCRIPTION

Autodock/Vina plugin for PyMOL can be used to set up docking and virtual screening with AutoDock Vina and to view the results.

::DEVELOPER

Daniel Seeliger

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Autodock/Vina plugin for PyMOL

:: MORE INFORMATION

Citation

Daniel Seeliger and Bert L. de Groot.
Ligand docking and binding site analysis with PyMOL and Autodock/Vina.
J. Comput.-Aided Mol. Des. 24:417-422 (2010)

AUDocker 1.1.2 – GUI for AutoDock Vina

AUDocker 1.1.2

:: DESCRIPTION

AUDocker is a GUI for AutoDock Vina. helps in virtual screening of huge number of ligands continuously. Helps in resumption of work in accidental shutdowns. This program can help you in docking several ligands automatically in to a prescribed protein receptor site.

::DEVELOPER

Dr M Murali Krishna Kumar

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 AUDocker 

:: MORE INFORMATION

Citation

BMC Res Notes. 2011 Oct 25;4:445. doi: 10.1186/1756-0500-4-445.
AUDocker LE: A GUI for virtual screening with AUTODOCK Vina.
Sandeep G, Nagasree KP, Hanisha M, Kumar MM.

MOLA – System for Virtual Screening using AutoDock4/Vina on Computer Clusters

MOLA

:: DESCRIPTION

MOLA  is an easy-to-use software for Virtual Screening (VS) in a non-dedicated computer cluster using AutoDock4/Vina. Several tasks needed for AutoDock4/Vina are automated with MOLA including: ligand preparation, AutoDock4/Vina jobs distribution, result analysis and ligand ranking. A Graphical User Interface (GUI) is used for easy selection of parameters and easy handling of input/output files generated in a VS project. MOLA is integrated in a Live-CD GNU/Linux Live Distribution designed to boot from the CD on any available computer without ever using the computer hard-disk drive. When a VS project is finished the computers can be restored to the original operating system by simply removing the CD and restarting.

::DEVELOPER

Hugo Froufe and Rui Abreu

:: SCREENSHOTS

:: REQUIREMENTS

  • CDROM

:: DOWNLOAD

 MOLA

:: MORE INFORMATION

Citation

Rui MV Abreu, Hugo JC Froufe, Maria João RP Queiroz, and Isabel CFR Ferreira
MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
J Cheminform. 2010; 2: 10.

AutoDock Vina 1.1.2 – Molecular Docking and Virtual Screening Program

AutoDock Vina 1.1.2

:: DESCRIPTION

AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.

::DEVELOPER

Dr. Oleg Trott , in Molecular Graphics Laboratory , The Scripps Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

AutoDock Vina

:: MORE INFORMATION

Citation

O. Trott, A. J. Olson,
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading,
Journal of Computational Chemistry 31 (2010) 455-461