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MSM_bind is an open source Python package to analyse molecular dynamics simulations in order to predict the binding site of drug fragments. In particular, it includes algorithms for:
- Clustering and Featurization
- Markov state models (MSMs)
- Residence time analysis
- Kinetic clustering
- Uncertainty estimation
MSM_bind can be used from Jupyter or by writing Python scripts. For a tutorial, please check the MSM_bind Tutorial jupyter notebook and use the example simulations in the traj folder.
We are planing to include pip and conda installation in the future. Until then, download the MSM_bind.py script.
For bug reports/suggestions/complaints please file an issue on GitHub
- pyemma 2.3.2 (https://github.com/markovmodel/PyEMMA)
- pmx (https://github.com/dseeliger/pmx)