Interestingly contribution of internal energies to the free energy was very significant for Leu941, this indicates that final conformation of Leu941 is more favourable upon binding to H3K4me3 and H3K9me3 peptides.
Synthetic inhibitors and biological ligands form two distinct subpopulations in the data, with the former having greater average affinity due to more favourable entropy changes on binding.
Gln-89 side chain also limits bacterial interaction and its substitution to shorter side chains (Q89A and Q89N) is more favourable especially for Rd-CEACAM binding.
Loop-based structures have been reported to be more favourable for highly effective siRNA binding [ 15], but we found again that they were not predictive of silencing efficacy (Table 2).
This has been attributed to a specific counterion binding which should be more favourable in a medium with a lower dielectric constant and of a lower solvation energy.
With the phosphate in the −2 state the binding energy is 1.8 kcal/mol more favourable than for the −1 state, corresponding to a 20-fold higher affinity.
However, in a previous in vitro study of this fragment, we could demonstrate that the binding characteristics of 111In-Fab were more favourable than those for 125I-Fab, even in a non-internalizing setting, resulting in longer retention of 111In-Fab compared to that of 125I-Fab on SCC cells [31].
Occupation of the same minor binding pocket of CXCR3 with a compound with more favourable pharmacokinetics is perhaps worthy of further investigation.
Conversely upon methylation of Lys, PABC is predicted to provide a more favourable interaction site for the eRF3-N PAM2 motif than when unmodified, whereas binding of the PAIP2 PAM2 does not appear to be significantly affected.
On the other hand, the third generation SUs gliclazide and glimepiride have different receptor binding properties, reducing the risk of hypoglycaemia and are potentially more favourable treatment alternatives [ 24, 25].
