Figures 2...7

Scripts for creating the figures made in the manuscript Binding Position Dependent Modulation of Smoothened Activity by Cyclopamine

Run pdb3.py before running the codes listed in each directory.

Supplementary

Scripts for generating Supplementary information include MSM construction, VAMP2 score calculation, Chapman-Kolmogorov test, and KL divergence.

Alchemical Binding Free Energy Analysis (Figure 2b)

Performed by using python alchemical_calculation.py available at Prof. Mobley's alchemical analysis library