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I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their respective labs. What is an appropriate error margin so that I can compare these two results?

I just came across this article.

Now let me quote the following from the article.

Note that we generally require predictions to be within 1 kcal/mol to be useful, since 1.4 kcal/mol equates to a 10-fold difference in binding affinity.

Can we use this 1 kcal/mol as the acceptable error margin?

Edited:

from *(lehninger principles of biochemistry) and Is Kd (the dissociation constant) for a given protein-ligand pair directly correlated to binding affinity (kcal/mol, Rosetta Energy Units, etc.)?

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    $\begingroup$ "... both Group A and B have determined the lowest free energy of the same protein in their respective labs .... " do you mean theoretically or empirically ... in both cases I would like to know more about standard ways to achieve that nowadays $\endgroup$
    – pippo1980
    Commented Nov 25, 2023 at 9:39
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    $\begingroup$ talking about "The maximal and current accuracy of rigorous protein-ligand binding free energy calculations" nature.com/articles/s42004-023-01019-9 ---> ...As our experimental reproducibility survey indicated that experimental RMSE is on average ~1 kcal mol−1, it would be an extraordinary challenge to ever have an FEP method that achieves an error truly statistically indistinguishable from the experimental error o.... So again is the error margin sought a theoretical or empirical one ?? $\endgroup$
    – pippo1980
    Commented Nov 25, 2023 at 10:01
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    $\begingroup$ what kind of chemical interaction gives rise to a change of 1.4 kcal/mol ?? $\endgroup$
    – pippo1980
    Commented Nov 25, 2023 at 13:04
  • $\begingroup$ @pippo1980, I had empirical determination in mind. $\endgroup$
    – Omar Shehab
    Commented Nov 25, 2023 at 13:32
  • $\begingroup$ @pippo1980, I do not know what kind of chemical interaction gives such rise. Sorry. $\endgroup$
    – Omar Shehab
    Commented Nov 25, 2023 at 13:33

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