NR_MSM

Markov state model (MSM) analysis of nuclear receptor molecular dynamics simulations, from the study of allosteric signal transduction in FXR/RXR heterodimers bound to steroidal antagonists (see FXR-RXR_analysis).

Contents

File	Description
MSM_NR-gmf.ipynb	PyEMMA workflow: featurization, dimensionality reduction, clustering, implied timescales, Chapman–Kolmogorov test and metastable states

Requirements

Python 3 with Jupyter and the libraries listed below. Trajectories and Schrödinger Suite outputs are not included in this repository.

pip install jupyter numpy matplotlib pyemma mdtraj nglview mdshare

Author

Glaucio Monteiro Ferreira — Research Associate, Institute of Chemistry, University of São Paulo (IQ-USP) · LIBNM · Ferreira Lab · ORCID · FAPESP profile · gmf@usp.br