EXP-101 Lecture 1: _A_SIMPLE_PROTOCOL_TO_PERFORM_DOCKING

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19 Jun 2022
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Requirements: windows xp or windows 7 freely available software"s for non-commercial uses, moe, mgl tools http://mgltools. scripps. edu/downloads, cygwin http://www. cygwin. com/install . html (click setup-x86. exe for 32-bits version while setup- x86_64. exe for 64-bits version, pymol https://pymol. org/2/#download, discovery studio visualization https://www. 3ds. com/fileadmin/products- Extract autodock. exe and autodock. exe file to cygwin/home/folder 1. Again copy paste autodock4 and autogrid4 scripts to cygwin/bin. Retrieving target. pdb files from major protein databases http://www. rcsb. org/pdb/home/home. do. Now copy cygwin home foler1 path from os (c) Delete selected chain (*never remove co-crystalized solvent from target eg: heavy metals, nadph) Select highest energy amino chain and apply then close. Confirm stability ensuring majority of amino acid in favorable region. If majority r in unfavorable region then change force field and start energy minimization from start. Search your lead molecule in pubchem or draw 2d structure in chemdraw and convert it into 3d form in chemdraw3d. Save as ligand. pdb in cgywin/home/folder 1: preparing pdbqt format for target and ligand (target. pdbqt, ligand. pdbqt), grid.

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