SurA

Markov state model (MSM) analysis of molecular dynamics simulations of SurA, a periplasmic chaperone of Gram-negative bacteria.

Contents

File	Description
MSM_SurA.ipynb	PyEMMA workflow: featurization, dimensionality reduction, clustering, implied timescales 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