For each protein structure, the ligand binding site was defined as a box measuring 30Å in each dimension, centered on the centroid of the co-crystallized ligand. The centroid was computed with the RDKit Chem.rdMolTransforms.ComputeCentroid function, considering the heavy atom coordinates (note that all protein structures of DUDE-Z have exactly one co-crystallized ligand, regardless of the number of ligand binding pockets present in the structure).