With the aid of the automated molecular docking, the inhibition effect of 20(S)-Protopanaxadiol (PPD) and Ginsenoside Rh2 for CYP2C9 and CYP3A4, respectively, were studied by InsightII/Affinity program and the docking complexes were analyzed by InsightII/Ludi program. The results indicate that PPD is a competitive inhibitor for CYP2C9 but a poor inhibitor for CYP3A4, Rh2 is a noncompetitive inhibitor for CYP3A4, but a poor inhibitor for CYP2C9. Hydrophobic PPD is stabilized in the center of the substrate-binding regions of CYP2C9 by hydrogen bond and has strong interactions with heme and the key residues in active site which play important role for binding the substrate. Theoretical K-i value was calculated to be 26.7 mu M by using Ludi score 457 of CYP2C9-PPD complex. As hydrophilic Rh2 is away from the substrate-binding regions of CYP3A4, it has very weak interactions with the key residues in the active site. But the docking of Rh2 makes the conformation of CYP3A4 to change, including the position of a key residue Ser119 that leads to a decrease in catalytic activity. Theoretical K-i value is 102.8 mu M by using Ludi score 398 of CYP3A4-Rh2 complex. The theoretical results are in well agreement with the experimental results. (c) 2007 Elsevier Ltd. All rights reserved.