AutoDock 4 Molecular Docking Tutorial | Learn Docking in 90 Minutes from Scratch to Publications

All the bioinformaticians out there, you know how to use AutoDock 4 and how to do molecular docking analysis by using AutoDock Vina or AutoDock 4 by using MGLTools, okay? So, today we are going to learn how to use AutoDock 4 and this will be a comprehensive tutorial starting from the installation to the settings to the

protein and the ligand confirmations. So, we can go ahead by uh downloading the software from the uh website of MGLTools or the Scripps Research Institute. We can install it and then we have to tweak some settings for AutoDock 4. Then we go ahead for the protein and the ligand uh you know, uh

we are going to download uh it from different databases and how to proceed further. Okay? The next thing that we are going to do is how to actually prepare the target, prepare the ligand, and how to set up the grid, and how to set up the parameter file. Uh these are the main four steps in

AutoDock 4 or AutoDock Vina or uh whoever is doing molecular docking, these four settings are required to do molecular docking analysis, okay? The next step that we are going to do is the actual docking and to analyze the confirmations, the interactions, and capture some high-quality images uh from MGLTools or AutoDock 4 software for

publication-quality figures. And uh this will be uh as I said, this will be a comprehensive uh tutorial which lasts for I think 1 hour or something. And we can quickly go through the theory behind AutoDock 4. Why we are using AutoDock 4. Many people I mean all the bioinformaticians out there, they know

how to do molecular docking analysis, but some people they lack the understanding of the you know, actual technique of what is going on behind. What is the black box behind the AutoDock 4 that we need to you know, know. So, basically this AutoDock 4.2 uses a semi-empirical free energy force field to evaluate the