- Install autodock vina and MGLTools (http://vina.scripps.edu/manual.html#linux)
- Download PDB receptor file and store in data/receptors
- Write configuration file for Vina as in http://vina.scripps.edu/manual.html#config , starting with receptor = tmp/receptor.pdbqt ligand = tmp/ligand.pdbqt
Running one of the following scripts will preprocess receptor and ligands, run docking with parameters specified in 'conf', and write outputs (score and docking time per molecule) to csv file. If required several binding modes, the score in csv is the average of the N top modes.
If molecules have their SMILES written in myligands.txt , run :
python dock_txt.py -t [pdb_target_prefix] -i [myligands.txt] -o [my_csv_output.csv]
SMILES stored in a csv file with header row, SMILES in 'can' column. Run :
python dock_df.py -t [pdb_target_prefix] -df [myligands.csv] -o [my_csv_output.csv]