Figure 3.

PopShift performs well as one varies the amount of simulation data, whereas traditional “best score” ensemble docking gives worse performance and has greater statistical variation as data is added. The data set used for MSM construction was truncated by taking the indicated fraction from the beginning of each trajectory. This can be viewed as asking the question, “what would happen if simulations had been stopped early?” The error bars arise from the standard uncertainty in the mean across the three replica data sets.