We benchmarked the CANDOCK hierarchical docking algorithm using a benchmarking set (1) to determine whether the algorithm can reproduce the crystal binding pose of the ligand in the binding site of the protein and (2) to correlate the scores of the threedimensional (3D) docked poses of the ligand to the measured Kd/Ki values of the ligand binding with the protein. PDBbind benchmark 36 is very well suited for this analysis because, for each protein in this set, it provides 3D coordinates and corresponding activity values for five protein-ligand complexes. In the PDBbind v2016 core set, there are a total of 285 such complexes for 57 proteins of interest to the medicinal chemistry community. The number of fragments present in a given ligand range from a single fragment to ligands consisting of thirteen fragments, enabling an evaluation of our method on both rigid and flexible ligands.