Scripts for calculating the posterior distribution of ln PF model parameters as described in Wan et al. JCTC 2020
experimental-data - Experimental HDX protection factors (ln PF) data for ubiquitin and BPTI
simulation-data - Analysis of <N_c> and <N_h> from D.E.Shaw trajectory data
posterior - scripts to do the posterior sampling of ln PF forward model parameters
The scripts are written in python 3 Jupyter notebooks.
The Anaconda python distribution is recommended: https://www.anaconda.com/distribution/ . You will need:
- Jupyter
numpypandasmatplotlibfor plotting and visualization
Hongbin Wan, Yunhui Ge, Asghar Razavi and Vincent A. Voelz. Reconciling Simulated Ensembles of Apomyoglobin with Experimental Hydrogen/Deuterium Exchange Data Using Bayesian Inference and Multiensemble Markov State Models J. Chem. Theory Comput. 2020, 16, 2, 1333-1348 https://doi.org/10.1021/acs.jctc.9b01240