AutoDock Vina Extended

Publisher: OneAngstrom

Updated: June 28, 2022


Latest versions

Windows: 3.4.5 on SAMSON 4.0.0

Linux: 3.4.5 on SAMSON 4.0.0

Mac: 3.4.5 on SAMSON 4.0.0

3920
694
Non-euro prices are given for information purposes only.
The reference price is the one in euros.

Free trial

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Monthly plans

Academic
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$15.79 / mo
Commercial
$157.90 / mo

Yearly plans

Academic
Sign in with an academic email address for this rate
$157.90 / year
Commercial
$1,578.98 / year
Any question? Send us an email at sales@oneangstrom.com or schedule a short call.

AutoDock Vina Extended

Publisher: OneAngstrom

Updated: June 28, 2022


Latest versions

Windows: 3.4.5 on SAMSON 4.0.0

Linux: 3.4.5 on SAMSON 4.0.0

Mac: 3.4.5 on SAMSON 4.0.0

3920
694
Dock thousands of ligands into proteins and rank them with AutoDock Vina.

New: join the AutoDock Vina Extended community at https://s-c.io/aved !

AutoDock Vina is a highly popular protein-ligand docking program.

Its integration in the SAMSON platform offers an extensive range of additional functions and makes it extremely easy to setup calculations, dock large libraries of ligands, and analyze results.

Benefits

  • Easily specify receptor’s flexible side chains.
  • Easily activate and deactivate bond torsions.
  • Interactively set the search grid based on the receptor or binding sites.
  • Automatically minimize ligands before docking.
  • Automatically lock bond types based on chemical properties.
  • Dock, score, or locally optimize ligands without docking.
  • Export PDBQT input files.
  • Interactively compare docking results.
  • Export results as conformations, structures, tables, logs, CSV, etc.

Usage

AutoDock Vina Extended has two main use modes:

Single ligand

  1. Select the receptor, the flexible side chains, and the ligand. Toggle rotatable bonds on and off by clicking on their associated controller. By default, all bonds in the ligand and flexible side chains will be considered to be fully flexible.
  2. Adjust the search grid through the GUI based on the whole receptor or binding sites or by directly moving the grid vertices with the mouse
  3. Set the docking parameters (exhaustiveness and the maximum number of modes wanted, etc.) and click the "Dock ligand" button.

A new folder containing binding modes stored as conformations will be added to the document. Double click on conformations in the document view to restore the corresponding atom positions.

Ligand library

  1. Select the receptor and the flexible side chains. Toggle rotatable bonds on and off by clicking on their associated controller.
  2. Select the folder containing the ligands. All ligands will be considered to be fully flexible.
  3. Adjust the search grid through the GUI based on the whole receptor or binding sites or by directly moving the grid vertices with the mouse
  4. Set the docking parameters (exhaustiveness and the maximum number of modes wanted, etc.) and click the "Dock library" button.

A new folder containing the top ligands will be added to the document, and the top binding modes will be stored as conformations.

Double click on conformations in the document view to restore the corresponding atom positions.

See this page for a complete tutorial.

Reference

[1] 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.

AutoDock Vina Extended is an extension for SAMSON,
the integrated platform for molecular design.

To use AutoDock Vina Extended:

1. Create your free account and choose a molecular design plan
2. Download and install SAMSON on your computer
3. Come back to this page to add the extension to your account


When you restart SAMSON, the extension will be automatically installed
and will be usable directly from within SAMSON.