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AutoDock Vina is a top-rated protein-ligand docking program.

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

This extension integrates AutoDock Vina v.1.2.5.

Benefits

• Easily specify the 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 in ligands based on chemical properties.
• Dock, score, or locally optimize ligands without docking.
• Generate a project with PDBQT input files if you want to run it on your cluster.
• 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.

Documentation

See this page for a complete tutorial.

Reference

[1] Eberhardt, J., Santos-Martins, D., Tillack, A.F., Forli, S. (2021). AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. Journal of Chemical Information and Modeling.

[2] 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.