Molecular Docking for Beginners | Autodock Full Tutorial

This tutorial will introduce you to docking using the AutoDock suite of programs. We will use a Graphical User Interface called AutoDockTools, or ADT, that helps a user easily set up the two
molecules for docking, launches the external number crunching jobs in AutoDock, and when the dockings are completed also lets the user interactively visualize the docking results in 3D.

The molecular docking approach can be used to investigate interaction between a small molecule and a protein at the atomic level, which allow us to understand the behavior of small molecules in the binding site of target proteins, and biochemical mechanism in protein and ligand molecule.

Sections:
0:00-2:00 Requirements
2:01-8:45 Theory
8:46-10:40 Installation of MGLTools
10:44-19:37 Protein and Ligand download and cleanup
19:38-28:20 Protein preparation using MGLTools
28:25-34:42 Ligand preparation using MGLTools
34:43-40:23 Grid box settings
40:25- 51:03 Running Autogrid4
51:05-59:25 Docking parameters
59:29-1:08:25 Running AutoDock4
1:08:26-1:29:30 Analyze conformations
1:29:32-1:43:38 Create publication quality figures using ChimeraX
1:34:38-1:37:43 Using Discovery studio for 2D interaction plot
1:40:00-1:43-34 Evaluation and comparison with experimental PDB structure
1:43:39-1:49:39 Inhibition constant Ki

AutoDock 4.2.6: https://autodock.scripps.edu/download...
MGL tools: https://ccsb.scripps.edu/mgltools/dow... (v.1.5.7)
MGLTools 1.5.6 documentation: https://ccsb.scripps.edu/mgltools/1-5-6/

Music

Almost in F - Tranquillity by Kevin MacLeod is licensed under a Creative Commons Attribution 4.0 license. https://creativecommons.org/licenses/...

Source: http://incompetech.com/music/royalty-...

Artist: http://incompetech.com/

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AutoDockTools:
A Tutorial #AutoDock 4 Tutorial | Installation to Publication #Using autodock tools for docking