The qfvina.x application calls the third-party program mk_prepare_ligand.py from Meeko for ligand preparation and to obtain the input ligand in the necessary PDBQT format for AutoDock Vina docking, as well as the mk_export.py program to export the results to standard SDF format. It also calls wk_prepare_receptor.py from the Waterkit program cite followed by mk_prepare_receptor.py for the necessary protein preparation for AutoDock Vina. The exhaustiveness parameter for AutoDock Vina was set to 32 for all docking runs. We kept the top 5 docking poses for all conformations in QFVina and QFVinardo runs, and the top 50 docking poses for traditional Vina and Vinardo flexible ligand docking. Although this is likely overkill and the storage space for results could be reduced by decreasing these values in future projects, I retained these values for safety.