Review AutoDock Vina Extended
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AutoDock Vina Extended

Publisher: OneAngstrom

Updated: August 30, 2019


Latest versions

Windows: 0.8.3 on SAMSON 0.8.5

Linux: 0.8.3 on SAMSON 0.8.5

Mac: 0.8.3 on SAMSON 0.8.5

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Monthly plans

Academic
14,90 € / mo
Commercial
37,90 € / mo

Yearly plans

Academic
149,00 € / year
Commercial
379,00 € / year

AutoDock Vina Extended

Publisher: OneAngstrom

Updated: August 30, 2019


Latest versions:

- Windows: 0.8.3 on SAMSON 0.8.5

- Linux: 0.8.3 on SAMSON 0.8.5

- Mac: 0.8.3 on SAMSON 0.8.5

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

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

Usage

This SAMSON Element has two use modes.

Single ligand

  1. Select the receptor, the flexible side-chains and the ligand. Select the Use Editor (Home / Use, shortcut U) to toggle rotatable bonds on and off by clicking on their associated controller.
  2. Adjust the search grid through the GUI or by directly moving the grid vertices with the mouse
  3. Set the docking parameters (exhaustiveness and the maximum number of modes wanted) and click the "Dock ligand" button.

Binding modes are generated both as structural models and conformations. Double click conformations in the document view to restore the corresponding atom positions.

Ligand library

  1. Select the receptor and the flexible side-chains. Select the Use Editor (Home / Use, shortcut U) to 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 or by directly moving the grid vertices with the mouse
  4. Set the docking parameters (exhaustiveness and the maximum number of modes wanted) and click the "Dock library" button.

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