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AutoDock Vina

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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AutoDock Vina

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

Perform protein-ligand docking thanks to AutoDock Vina.

This SAMSON Element wraps the popular protein-ligand docking program AutoDock Vina.

Usage

  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 button.

Binding modes are generated both as structural models and conformations (right click on a conformation node in the document view to restore the corresponding atom positions).

See the AutoDock Vina Element tutorial for more information.

Note: for docking libraries of ligands instead of individual ligands, please refer to the AutoDock Vina Extended element.

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.