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 - 01:30:03 PDT
