> A residue-based dielectric model is recommended by one reviewer for my work
> to improve the accuracy of MMGBSA calculations. My work was to study
> simulation based folding of proteins and what factors contribute to
> folding. Can someone help me with the details what exactly is referred here
> to imply?
Hmmn, either the reviewer is potentially confused or there is a
misunderstanding or I am seriously confused which is distinctly possible.
I have not heard of a residue-based dielectric model and this would not
seem to me to make much sense (since dielectric screening is related to
the (solvent) environment, context, and surroundings. It is not related
to the residue type). A search of PubMed for "residue-based dielectric"
turns up one paper that although good and related does not do residue
based dielectric screening or treatment.
Perhaps you mean residue-based decomposition of the (crude) MM-GBSA
energies? This will not improve accuracy but potentially provide insight
into the relative importance of specific residues to the overall (free)
energetic landscape you are trying to discover? Read the Amber manuals
with respect to idecomp potentially both in MM-PBSA/MM-GBSA and TI
conceptualizations.
--tec3
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Received on Fri Apr 21 2017 - 18:30:03 PDT
