Personally, I would not trust GB calculations to give me anything
reliable for such a system. Protein-DNA complexes are typically
stabilized by interactions of basic residues with phosphates- and
these are known to be problematic in most GB models. You don't say
which residue is mutated to Ala, but if it's Arg then my feeling would
be not to expect much accuracy.
Why not use PBSA for this? Are you following something in the
published literature where GB was shown to work well in DNA binding
energies? As always, you need to either follow the published
literature (with care, it often has weaknesses) or understand well the
limitations of the models. With GB, the main limitation is in exactly
what's important for what you are trying to study. I wouldn't use it.
On Tue, Aug 9, 2011 at 4:04 AM, Catein Catherine <askamber23.hotmail.com> wrote:
>
> Dear Sir/Madam,
> In another sets of calculations, I have calculated the binding energy (GBTOT) for several protein-DNA complexes, these complexes are structurally similar with one of the interacting residues being mutated to alanine.
> Given the DS was not calculated, can I confidently comments on their RELATIVE GBTOT energy?
> What about if I want to compare the binding energy in a protein-DNA complex with a protein-protein complex? Since these two complexes are structurally dissimilar, is it a must to calculate DS for each complexes before doing doing this comparison? However, I have heard that calculating DS for large complexes are computationally demanding, and the accuracy of DS is not very high. Thus, overall, what is the common practice to get the GBSA binding energy comparison for protein-DNA and protein-protein complexes?
> Best regards,
> Catherine
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Received on Tue Aug 09 2011 - 04:30:03 PDT
