On Wed, Sep 14, 2016, hari krishna wrote:
>
> We have carried microsecond simulations for a protein (800 aa) - RNA (17
> bp) systems. Various modified RNA molecules have been used to find the
> binding specificity/affinity with the same protein. The free energy of
> binding was calculated using MM-PBSA method. The entropic contribution was
> calculated using NMODE method. The free energy values (dG) are in the
> range of -250 kcal/mol.
It's not clear from your email what you mean by "dG": is this the estimated
value for the protein-RNA association energy? If so, something is seriously
amiss. If you are making errors of hundreds of kcal/mol in the aboslute
binding affinities, it's hard to be sure that these errors will all cancel
in the ddG calculations.
I understand that many people in our field assume that there will be this sort
of error cancelation, so that ddG values might be useful even where the
underlying dG values are not. But I have never been at all happy with this
idea: there is a fair likelihood that some really important feature (specific
metal ion effects?) is missing from the model.
.....dac
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Received on Wed Sep 14 2016 - 07:00:04 PDT
