Introduction to using AutoDock Vina for determination of receptor-ligand binding affinity

Hey guys, I have somewhat recently come across AutoDock Vina and found it a great program for certain applications, and wanted to share some basics on how to use the program including its molecular viewer AutoDockTools.

AutoDock Vina:
https://vina.scripps.edu

MGL Tools:
https://ccsb.scripps.edu/mgltools/

Protein Data Bank:
https://www.rcsb.org

Please cite these articles if using AutoDock Vina:
(1) J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli. (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

Content:
0:00 Introduction & Downloading
2:19 Finding and visualizing biomolecules
5:12 Preparing molecules for use in AutoDock Vina
9:20 Running calculations with AutoDock Vina
16:14 Interpreting results

Thanks for watching!