Examples of ligand identification using the proposed MinkLoc3Dv2 model. (A–D) Examples of correctly predicted X-ray ligands. (E) Uridine-5ʹ-diphosphate (UDP) misclassified as uridine (URI, black dashed frame). (F–I) Examples of correctly predicted cryoEM ligands. (J) Heme A (HEM) misclassified as a rare ligand due to incorrect density thresholding. Each ligand is labeled by its Chemical Component Dictionary ID, structure resolution, and (in parentheses) the PDB ID, chain, and residue number. X-ray diffraction ligands (A–E) shown in green mesh based on F_o–F_c maps contoured at 2.8σ calculated after removal of solvent and other small molecules (including the ligand) from the model. CryoEM ligands (F–J) depicted in pink mesh based on difference maps contoured according to the proposed automatic density thresholding method (13.642, 3.385, 17.997, 7.850, and 5.613 V for panels F–J, respectively). The white mesh in panel J shows a manually selected contour threshold of 11.000 V. Atomic coordinates were taken from the PDB deposits.