MCCS example for SARS-CoV-2

This repository contains the intermediate and output data involved in the process of MCCS virtual screening against the determined SARS-CoV-2 3CL structure using approved drugs on DrugBank.

1_drugbank_smiles

This directory contains two lists of small molecular SMILES extracted from the DrugBank database. One is of all drugs and the other approved drugs.

The original DrugBank database was downloaded on January 3, 2020.

2_covid19_structure_[step1,2,4]

This directory contains the receptor and ligand PDB files splitted from the crystal structure of COVID-19 main protease (3CL) in complex with an inhibitor N3 (PDB ID - 6LU7), as well as converted PDBQT files and predicted pKa values for the ligand.

3_drugbank_pdbqt_[step5,6,7]

This directory contains the converted PDBQT files and predicted pKa values for all drugs on DrugBank.

4_covid19_scoring_output_[step9]

This directory contains the jdock scoring output (residue energy contribution vectors represented in .csv and conformations represented in .pdbqt) of the covid19 complex. The script used to acquire this looks like

jdock -r receptor.pdbqt -l ligand.pdbqt -o covid19_scoring_output -sp

5_drugbank_docking_output_[step10]

This directory contains the complete jdock docking output (residue energy contribution vectors represented in .csv and conformations represented in .pdbqt) for the approved drugs on DrugBank. The script used to acquire this looks like

jdock -r receptor.pdbqt -l drugbank_pdbqt $(pdbm -L ligand.pdb) -o drugbank_docking_output

Note that some of the input ligands did not succeed in docking and are not included in this directory. The number of successful results is 1,814.

6_similarity_search_output_[step11]

This directory contains the complete output of mccsx similarity search in the DrugBank approved library for the COVID-19 vector pattern. The script used to acquire this looks like

mccsx search -l drugbank_docking_output -p covid19_scoring_output -o similarity_search_output