Figure 7.

Population shift calculated by PopShift correctly favors pocket conformations with a low α carbon RMSD for the holo crystal structure. The data histogrammed is the RMSD of the predicted pocket conformation to the holo crystal structure’s pocket, where the structures are superimposed according to an alignment of their pocket atoms but not any ligand atoms. For each main panel, the three subpanel columns represent individual replica data sets. The top row shows the ligand-free equilibrium RMSD distributions and the lower row shows how the population is redistributed in the presence of ligand. Main panel A provides the data for benzene, while main panel B provides the data for n-butylbenzene.