This repo contains Jupyter notebooks (former IPython) for PyEMMA. Currently there are examples for applications and methods.
- Markov state model for Pentapeptide system
- Markov state model for BPTI
- Protein-ligand binding: Hidden Markov model analysis of Benzamidine-Trypsin binding
- Input feature selection
- Model selection and validation
- Transition path theory
- Augmented Markov models
- Doublewell potential
- Alanine dipeptide
