Fig. 4

a Comparison of the Hungarian algorithm against DockRMSD for the 3112 molecules whose RMSD was underestimated by the Hungarian algorithm. b Comparison of the Hungarian algorithm against DockRMSD for the 190 molecules whose RMSD was underestimated by the Hungarian algorithm in the native ligand pose benchmark. c An example pair of poses where the Hungarian algorithm grossly overcorrected for symmetry due to its insensitivity to global molecular topology (Ligand PDB ID: BEG; Receptor PDB ID: 1D4I [25]). Interpose correspondence between central carbon atoms and nitrogen atoms is drawn to represent the source of the RMSD disagreement. Hungarian correspondence is drawn in red to demonstrate that the correspondence should not be allowed according to the chemical inequivalence of the atoms bonded to each atom of the pair