Fig. 3

a Ligand RMSD calculated by DockRMSD versus that by the naïve RMSD calculations on 1321 ligand molecules with symmetric structures. b An example pair of poses where naïve RMSD calculation failed to provide the optimal RMSD due to molecular symmetry (Ligand PDB ID: E10; Receptor PDB ID: 1H22 [23]). Interpose correspondence between oxygen atoms is drawn to represent the source of the RMSD disagreement by different methods