This repository contains data analysis code used for the strigolactone binding paper.
Related to Fig. 3a-b, scripts used to compute and compare protein-ligand contact probabilities for the two proteins.
In-house code used to perform adaptive sampling, plot free energy landscapes, and compute protein-ligand and inter-residue distances.
Scripts to compute and validate Markov state models
Related to Fig. 6, scripts used to perform analysis of the binding pockets.
Related to Fig. 3e-f, scripts used to determine most frequently occuring residues at key sites.
Scripts to compute standard binding free energy from simulations using the method described in Buch et al., Proc. Natl. Acad. Sci. 2011