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Multiscale enhanced sampling (MSES) allows for enhanced sampling of all-atom protein structures by coupling with the accelerated dynamics of the associated coarse-grained (CG) model. In this paper, we propose an MSES extension to replace the CG model with the dynamics on the reduced subspace generated by a machine learning approach, the variational autoencoder (VAE).

As far as I understood:

  1. The combination of MSES and the accelerated dynamics of the corresponding CG model is a superior way of sampling AA protein structures.
  2. In this paper the author proposes a novel model as an extension to the MSES technique.
  3. This new model is supposed to replace dynamic CG models.
  4. ... ... ??

I haven't understood the last part of the quote.

However, in short:

Moritsugu offers an extension to multiscale enhanced sampling (MSES) so that dynamic CG models can be replaced using a machine learning technique called variational autoencoder.

Can anyone help me either by explaining or paraphrasing it?

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  • $\begingroup$ I gave my +1 long ago. Since it's been 6+ months since you asked the question, can you update us on the status of this question for you? Have you figured it out? Is it still worrying you? $\endgroup$ Dec 31, 2022 at 3:16
  • $\begingroup$ @NikeDattani, I haven't figured it out. $\endgroup$
    – user366312
    Dec 31, 2022 at 8:11
  • $\begingroup$ Okay, I've bumped it up to the top of our list of homepage questions, by adding the machine-learning tag, which should have been there in the first place :) Hopefully it will get an answer now! $\endgroup$ Feb 6, 2023 at 19:03
  • $\begingroup$ Since it has been almost 8 months since your last comment, I wonder how you have progressed with this problem? Have you found an answer, or found any other way to move forward in this research? Please update us! Is this still an active problem for you? $\endgroup$ Sep 30, 2023 at 19:47
  • $\begingroup$ @NikeDattani, It was needed when I was writing my PhD proposal. The proposal is submitted already. Hence, this is not an active problem for me anymore. $\endgroup$
    – user366312
    Oct 1, 2023 at 7:46

1 Answer 1

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Since this is not an active problem for the researcher anymore, I'm removing it from the unanswered queue, but if anyone wants to write another answer, please just comment here and I will remove this Community Wiki!

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