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In this video, I’ll demonstrate how to perform molecular docking of multiple ligands using AutoDock Vina, one of the most popular open-source docking tools in computational drug discovery.
We’ll start from the basics — preparing the protein and ligands, setting up the grid box, running docking for multiple ligands, and analyzing the results.

You’ll also learn how to interpret docking scores, visualize binding poses, and prepare your docked complexes for Molecular Dynamics (MD) simulations using GROMACS to study stability and dynamic behavior.

🧪 Covered in this video:

Introduction to molecular docking and AutoDock Vina

Preparing protein and ligand files

Setting up the grid box around the co-crystallized ligand

Running docking for multiple ligands

Analyzing docking poses and binding affinity results

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