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PyEMMA IPython Notebooks

This repo contains Jupyter notebooks (former IPython) for PyEMMA. Currently there are examples for applications and methods.

Applications

• Markov state model for Pentapeptide system
• Markov state model for BPTI
• Protein-ligand binding: Hidden Markov model analysis of Benzamidine-Trypsin binding

Methods

• Input feature selection
• Model selection and validation
• Transition path theory
• Augmented Markov models

Estimation with fixed equilibrium distribution

• Doublewell potential
• Alanine dipeptide