For docking with DiffDock-L, fresh copies of the PDB files listed in the DUDE-Z were obtained directly from the PDB and loaded into the Schrödinger Platform (version 2021-1) for preprocessing with Protein Preparation Wizard. The preparation steps included assigning bond orders, adding hydrogens, filling in missing side chains, removing water molecules, protonating residues at pH 7.4 using PROPKA, and restrainedly minimizing hydrogens using the OPLS4 21 force field.