Figures 2...7

Scripts for creating the figures made in the manuscript Cyclopamine modulates smoothened receptor activity in a binding position dependent manner

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