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: https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Requirements https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Theory https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Installation of MGLTools https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Protein and Ligand download and cleanup https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Protein preparation using MGLTools https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Ligand preparation using MGLTools https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Grid box settings https://www.seevid.ir/fa/w/ZVKKsK5DsCY- https://www.seevid.ir/fa/w/ZVKKsK5DsCY Running Autogrid4 https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Docking parameters https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Running AutoDock4 https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Analyze conformations https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Create publication quality figures using ChimeraX https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Using Discovery studio for 2D interaction plot https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY-34 Evaluation and comparison with experimental PDB structure https://www.seevid.ir/fa/w/ZVKKsK5DsCY-https://www.seevid.ir/fa/w/ZVKKsK5DsCY Inhibition constant Ki AutoDock 4.2.6: https://autodock.scripps.edu/download-autodock4/ MGL tools: https://ccsb.scripps.edu/mgltools/downloads/ (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/ #bioinformatics #tutorials #computational biology #molecular informatics #biophysics #molecular docking #beginners tutorial #how to do docking #molecular docking for beginners #UCSF chimera X #Discovery Studio Visualizer #Publication quality images #Using AutoDock 4 with AutoDockTools: A Tutorial #AutoDock 4 Tutorial | Installation to Publication #Using autodock tools for docking

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