I know that the following can be simulated:

  1. secondary/tertiary structure prediction
  2. protein-surface/protein-protein interaction tests
  3. protein-ligand binding test

I wonder if references or explanations could be given for these and any other things I've missed on this list.

What do we simulate with the molecular simulation of proteins in theoretical or academic research?

  • 4
    $\begingroup$ This is a fairly broad question, as there are wide variety of different properties that can be simulated for proteins. $\endgroup$
    – Tyberius
    May 21, 2022 at 12:04
  • $\begingroup$ @Tyberius perhaps each example can be explained in detail in separate answers (one-topic-per-answer). $\endgroup$ Dec 10, 2022 at 16:17
  • $\begingroup$ This is an area in which Camps works. If he doesn't answer it, I suggest to close the question as too broad. $\endgroup$ Feb 6 at 21:09
  • $\begingroup$ @NikeDattani, This was not broad at all. I just wanted a list. $\endgroup$
    – user366312
    Feb 6 at 21:12
  • $\begingroup$ I think when Tyberius said that it was broad, I agree with him, because the "list" would be broad :) $\endgroup$ Feb 6 at 21:14

1 Answer 1


As @Tyberius mentioned, you can study many different things using Molecular Dynamics simulations of proteins. My senior had studied the structure and dynamics of Intrinsically Disordered Proteins (IDPs) using MD simulations. You can refer to paper and paper to get an idea about what I just mentioned. You can also refer to this paper by Prof. Jagannath Mondal, where they studied the binding of an anti-cancer drug using MD simulations.


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