There are many reasons, but for the most part, it would be a miracle if
the values from a very simple model such as MMPBSA actually gave you
results comparable to experiments.
You should look at papers on the method and people using it to get a
sense of accuracy.
Of the things you can check are:
Are you using GB or PB? PB is much more reliable, but more expensive.
Are you computing entropies or just delta energies?
That could easily change the ordering of binding data.
Adrian
On 4/6/21 10:55 AM, Manisha wrote:
> [External Email]
>
> Hello,
> I have taken three different stretches of DNA to see their binding
> with my protein. When experimentally done, it shows that stretch 1 binds to
> the protein whereas stretch 2 binds with higher affinity while 3 does not
> bind at all as seen by their Kd values. However, when the binding energy
> for the same 3 DNA stretches was calculated for the protein using MMPBSA it
> showed that stretch 2 which exhibited maximum affinity in wet lab
> experiment showed significantly lesser value than stretch 1 in MMPBSA.
> Also, stretch 3 which did not show any binding in wet lab experiment,
> showed significant binding in MMPBSA. So, how reliable are the binding
> energy values calculated by MMPBSA? Also, why is there such a negative
> trend between the binding energy calculated from wet lab and MMPBSA?
>
> Sincerely,
>
> *Manish*
>
> *Ph.D. Scholar*
>
> Multidisciplinary Centre For Advanced Research and Studies
>
> Jamia Millia Islamia
>
> Delhi-110025
>
> Ph.no: 9518014737
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Apr 06 2021 - 09:00:02 PDT
