Covid Research: Molecular Docking using Chimera and Autodock Vina (2020)

#Covid #Docking #Chimera #AutodockVina #MolecularModeller
Covid Research: Molecular Docking using Chimera and Autodock Vina
(Preparation, Binding Center, Docking, Analysis)

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Topics
-Chimera and Autodock Vina using SAR COV-2 main proteinase (Covid)
-Preparation of ligand and protein
-Identifying Binding Center -Running Autodock Vina in Chimera
-HBonds Analysis
-Viewing 2D, 3D protein-Ligand interaction

Publication
Lee, V.S., Chong, W.L., Sukumaran, S.D., Nimmanpipug, P., Letchumanan, V., Goh, B.H., Lee, L.H., Zain, S.M. and Abd Rahman, N., 2020. Computational screening and identifying binding interaction of anti-viral and anti-malarial drugs: Toward the potential cure for SARS-CoV-2. Progress in Drug Discovery & Biomedical Science, 3(1).
http://www.journals.hh-publisher.com/index.php/pddbs/article/view/117/89

The directory for the vina executable file
By Default;
C:\Program Files (x86)\The Scripps Research Institute\Vina\vina.exe

Center of mass
Command: measure center #0 mark true

Binding site center
From DS Visualizer (x,y,z); -10.711837 12.411388 68.831286
From Chimera Center for 49 atoms (x,y,z); (-10.75, 12.33, 68.84)

Binding site (X, Y, Z) and add missing residues for molecular docking using DS Visualizer (2020)
Youtube: https://youtu.be/-CJVsTsCX94

Видео Covid Research: Molecular Docking using Chimera and Autodock Vina (2020) канала Molecular Modeller