How can Markov State Models be used for ligand-protein complex Molecular Dynamics simulations?
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3.6 years ago
skim ▴ 50

I am a novice structural bioinformaticist using Schrodinger Desmond, and I have used MD for ligand-protein complex Molecular Dynamics simulations. While my methods are pretty traditional, I have found that in http://folding.stanford.edu/dig-deeper/ Folding@home uses Markov State Models for folding. Since Markov State Models can produce similar results for a multi-microsecond simulation with multiple nanosecond simulations, how can people use them for ligand-protein complexes?
enter image description here
As seen in this image, ligand binding time may take as much time as folding. In this case, are there any tools or applications that can be used easily like traditional MD toolkits like GROMACs or DESMOND? Are there any resources about this?
Thank you very much.

structure molecular dynamics • 2.2k views
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Entering edit mode
2.6 years ago
db4 ▴ 10

I think you will have to use tools: PyEMMA or MSMBuilder builder. I am using Gromacs to run simulations and there is no MSM capability (to be confirmed though)

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