jacquesboitreaud/vina_docking

Python scripts for molecular docking of molecules vs DUDE protein targets, using Vina

Python scripts for AutoDock Vina

• 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.

Docking from SMILES in txt file :

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]

Docking from SMILES in csv file :

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]