Question: How can Markov State Models be used for ligand-protein complex Molecular Dynamics simulations?
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gravatar for skim
2.5 years ago by
skim50
skim50 wrote:

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 dynamics molecular • 1.4k views
ADD COMMENTlink modified 18 months ago by db410 • written 2.5 years ago by skim50
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gravatar for db4
18 months ago by
db410
db410 wrote:

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)

ADD COMMENTlink written 18 months ago by db410
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