Dataset DUDE-Z served as the benchmark data set. DUDE-Z covers 43 pharmaceutically relevant protein targets, each represented by 26 (FA10) to 123 (PARP1) experimentally verified ligands (Figure ) with activities measured as EC50, IC50, Ki, or Kd values of 1 μM or better. For each active compound, the data set includes up to 50 carefully selected decoy molecules. These decoys are selected by property matching with the active compounds based on physicochemical properties, including molecular weight, number of hydrogen bond donors and acceptors, number of rotatable bonds, and water-octanol partition coefficient (log P). As an enhancement compared to previous versions of the benchmark data set, the DUDE-Z decoy matching procedure ensures that the active verified ligand and its selected decoys have an identical net charge at physiological pH. Furthermore, to ensure that the decoys have a dissimilar topology to the active compounds, only molecules with an ECFP4-based Tanimoto similarity of up to 0.35 to any active compound are selected as decoys. In total, DUDE-Z consists of 2312 unique active ligands and 69,994 decoy compounds across the 43 target proteins. The following data were collected from the DUDE-Z for docking: