Figure 4.

Population shift calculated by PopShift correctly favors ligand poses with a low RMSD to the crystal structure. The data histogrammed is the symmetry corrected RMSD³⁵ of the predicted pose to the holo crystal structure, where the structures are superimposed according to an alignment of their pocket atoms but not any ligand atoms. The RMSD histogram here is across all of the heavy atoms after this alignment. For each main panel, the three subpanel columns represent individual replica data sets. The top row provides the ligand-free equilibrium probabilities, and the lower row shows how the population is redistributed in the presence of the ligand. Main panel A provides the data for benzene, while the second panel B provides the data for toluene.