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normal protein coarse grain model quality check

  • tanvipar123
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2 years 2 months ago - 2 years 2 months ago #9311 by tanvipar123
protein coarse grain model quality check was created by tanvipar123
I have successfully created a coarse grain model of UBQ1 protein using martini forcefield. My question is how I can assess the quality of my coarse grain model? Whether the coarse graining is done correctly or not? Is there any way I can validate my model?
Last edit: 2 years 2 months ago by tanvipar123.

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2 years 2 months ago #9312 by riccardo
Replied by riccardo on topic protein coarse grain model quality check
I'm not the protein expert around here but, for starters, you could look at the residue-resolved RMSF of the CG model versus the one of the AA model. E.g., see Figure 2 of www.sciencedirect.com/science/article/pii/S000634951930195X .

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  1. Force Fields
  3. Proteins
  5. protein coarse grain model quality check
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