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AutoDock Vina Extended

Publisher: OneAngstrom Developer

Updated: September 10, 2021


Latest versions

Windows: 2.0.1 on SAMSON 2.0.0

Linux: 2.0.1 on SAMSON 2.0.0

Mac: 2.0.1 on SAMSON 2.0.0

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

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Monthly plans

Academic
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$17.47 / mo
Commercial
$174.73 / mo

Yearly plans

Academic
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$174.73 / year
Commercial
$1,747.26 / year

AutoDock Vina Extended

Publisher: OneAngstrom Developer

Updated: September 10, 2021


Latest versions:

- Windows: 2.0.1 on SAMSON 2.0.0

- Linux: 2.0.1 on SAMSON 2.0.0

- Mac: 2.0.1 on SAMSON 2.0.0

Dock libraries of ligands into proteins and rank them with AutoDock Vina.

This SAMSON Element wraps the popular protein-ligand docking program AutoDock Vina, provides additional functionality, and makes it possible to dock entire libraries of ligands.

Functionality

  • Easily specify receptor’s flexible side chains.
  • Interactively set the search grid based on the receptor or binding sites.
  • Automatically minimize ligands before docking.
  • Score or locally optimize ligands without docking.
  • Automatically export results (ligands modes, a results table, logs).
  • Visualize results.
  • Import results as conformations for further analysis.

Usage

See the AutoDock Vina Extended Element tutorial for more information.

This SAMSON Element has two 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.

Reference

If you use this SAMSON Element, please cite:

[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.