We’ve been investigating deep learning-based protein-ligand docking methods which often claim to be able to generate ligand binding modes within 2Å RMSD of the experimental one. We found, however, this simple criterion can conceal a multitude of chemical and structural sins…
DeepDock attempted to generate the ligand binding mode from PDB ID 1t9b
(light blue carbons, left), but gave pretzeled rings instead (white carbons, right).