The best HGFE scored SILCS pharmacophore hypotheses with 6, 4 and 4 features, respectively, for (a) HIVPR, (b) FXa and (c) DHFR. Hydrophobic Arom|Alip, hydrogen-bond donor and acceptor features are shown by cyan, blue and red color wireframe spheres. Representative crystal structures for the protein and ligand are overlaid with the hypotheses for (a) HIVPR (PDB ID:1QBS), (b) FXa (PDB ID:1XKB) and (c) DHFR (PDB ID:3DFR). Regions of the protein occluding the view are removed from the visualization.