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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

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