Separating bound from unbound Microstates

markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

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Separating bound from unbound Microstates #1425

Closed and-tos closed 5 years ago

and-tos commented 5 years ago

Hi,

I am using PyEMMA 2.5.6 to analyze protein protein-ligand interactions. In this paper https://www.nature.com/articles/ncomms8653/#supplementary-information, the authors mention that they projected the featured trajectory using TICA and then separated unbound microstates. Since after TICA projection the contact map is reduced I was wondering how I can identify microstates that are unbound. Thanks a lot for any help!

thempel commented 5 years ago

You could manually define a coordinate that describes ligand binding. Since this is highly system dependent, I can't help you with that, but it could be one of your contacts, a set of contacts or a minimum distance between several atoms with a cutoff. Once you have this, you can essentially split your clustered micro states into bound and unbound.