How to run an AutoDock Vina Virtual Screen against SARS-CoV-2 Helicase (Nsp13) at Home

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This step follows on from Issue #2 where you will have prepared your ligands from SMILES strings using Gypsum-DL. For this virtual screen I have used the SARS-CoV2 helicase - holo complex, nsp13 which originated from this paper

The protein was converted to the .pdbqt format in Chimera 1.16; all Zn, Mg, ATP, water molecules, and the nucleic acid strand were deleted, missing hydrogens were added and charges were assigned according to Aff14. The protein .pdbqt file can be downloaded here: nsp13.pdbqt.zip

First things first, you need to save your ligand .pdbqt files to your virtual screening folder , then proceed to that folder using Ubuntu (Linux terminal for Windows);

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First, copy and paste your ligand .pdbqt files into you vina virtual screen folder:

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To run the virtual screen, we must invoke the perl script by typing:

perl vina_vs_linux.pl

Once you press enter, Vina will ask you for the ligand.txt file as input.

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To improve our docking accuracy, we will perform flexible residue docking using AutoDock Vina 1.2. This means that we will treat the amino acids at the ligand-receptor interface as having some flexibility/rotatable bonds without performing a molecular dynamics simulation for the entire protein.

Here are the interface residues that we will make flexible:

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The output log.txt file will contain the conformer docking scores;

To visually inspect the poses, open the following files in Biovia Discovery Studio 2021 or PyMol: 1) 5rmm.rigid.pdbqt 2) Output.pdbqt