Dear Dr. David Case:
Thank you for sharing your experience with me. I have found "in practical"
publications in which when researchers have enough experimental Kd data,
they use them to correlate with MM/PBSA potential energies (such as this
one: https://www.ncbi.nlm.nih.gov/pubmed/26216222 ). During the development
of a best protocol, they might include the conformational entropy from NMA
to see if the correlations would be better. Although at most of the time,
people eventually still decided to ignore NMA entropy due to 1. it doesn't
really improve correlation and 2. it is too time-consuming... And
sometimes, it is also because they are dealing with a large quantity of
ligands; hence, inclusion of NMA entropy is not so attractive considering
the time input.
In my cases, I am dealing with a small amount of compounds. So I still
carried out NMA to see if integration of entropy will bring a better
correlation... However I don't hold too much hope on that. Because I feel
like the errors arise from everywhere, from the MM/PBSA method itself, the
molecular FFs, to the trajectories I picked out for analysis...
Still, thank you a lot for clarifying basic theory and sharing in practical
experience. I really appreciate that!
Best,
Guqin
On Sat, Apr 22, 2017 at 8:38 AM, David Case <david.case.rutgers.edu> wrote:
> On Sat, Apr 22, 2017, Guqin Shi wrote:
> >
> > I am still struggling in the relationship between MM/PBSA energies and
> NMA
> > energies...
>
> In *practice*, the NMA energies are ignored: only the entropies are used.
>
> Whether this is the best procedure or not is an open question as far as I
> know. I don't recall seeing studies that explore making use of the
> vibrational energies in this context; (I might have missed something.)
>
> ....dac
>
>
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--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
https://www.linkedin.com/in/guqin-shi-029bb634
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Received on Sat Apr 22 2017 - 14:00:03 PDT
