A flowchart showing the protocol used for generating the 3D common pharmacophore models is shown in Fig. . The 3D common pharmacophores recapitulate the representative chemical features such as hydrogen bond acceptors and donors, aromatic rings, and aliphatic carbons, together with a set for special atom types (i.e., sulfur or halogen) present in the ligand set. From this analysis, 6 models were generated for P-gp substrates and 6 models for inhibitors. Each common pharmacophore model was then used to score VS results. For each molecule, a substrate pharmacophore score and an inhibitor pharmacophore score were obtained by averaging the scores obtained using the 6 sets of substrates and inhibitors pharmacophore models, respectively.