Figure 6

Prediction of binding poses by PharmDock. (A) Comparison between the docking performance of PharmDock with and without Monte Carlo (MC) optimization. The fraction of protein-ligand complexes that have at least one predicted pose within 2.0 Å RMSD to the native binding pose is displayed on the y-axis. The first two columns are the docking results using native conformer as the docking input. The last two columns are using the Omega-generated low-energy conformers as docking input. (B) Distribution of the RMSD_top. Native-Seeded: Docking was performed with the native ligand conformation seeded within the Omega-generated low energy conformations as input. Omega-Only: Docking was performed with only the Omega-generated low energy conformations as input.