For a large number of DELTA G binding (Complex - Receptor - Ligand) the standard deviation is > 2 when DELTA G is ~30kcal/mol
Translating DELTA G to dissociation constant, a 2kcal/mol difference (either way) would mean dissociation constants differing by two orders of magnitude from the mean.
To put it in a different way. If DELTA G binding for ligand 1 to receptor A is 30kcal/mol and DELTA G binding of ligand 2 to the same receptor is 28kcal/mol with a standard deviation of 2, can one infer that the receptor has higher binding affinity for ligand 1?
Furthermore, if one factors in DELTA S with SD 2 (or more) interpretation of the results becomes much more tenuous.
And last, but not least. I have obtained standard deviations varying between 2 and 5 for nmode DELTA S calculations involving different ligands with the same receptor but the same number of frame readings. Is this to be expected?
Looking forward to receiving any comments on the above,
Regards
George
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Received on Fri Sep 14 2012 - 01:30:03 PDT
