Fig. 2

Crystal pose (green) and second-best docking pose (cyan) for the ligand of the protein-ligand complex 1DRJ. The Hungarian method assigns the ring oxygen to an oxygen atom nearby (\(d = 1.6\,{\AA }\), grey) while the graph isomorphism method correctly maps one ring oxygen to the other (\(d = 3.3\,{\AA }\), yellow). The Hungarian method results in an artificially low RMSD of 1.00 Å, compared to the correct RMSD of 2.46 Å obtained with graph isomorphisms