Example of critical protein-ligand contact used as constraint in docking. The aspartate residue 189 of the specificity pocket in the trypsin active site forms strong hydrogen bonds with the amidinophenyl moiety of trypsin inhibitors (PDBID: 1BJU). An example inhibitor co-crystallized with trypsin is shown in green. Yellow dashes represent the hydrogen bonds. Red-white lines represent the favorable locations (subset of protein-based pharmacophores) where a hydrogen bond donor groups from the ligands can interact with the hydrogen bond acceptor groups of the Asp residue.