Comparison of protein ligand binding affinities for over 8000 ligands with 28 protein targets shows conclusively that the average ligand binding affinities are not linear with molecular size.
Furthermore, although experimental binding affinities are not available for each individual binding register, they can be estimated using the RTA sequence-based method [26] for the allotypes with sufficient available binding data.
It is also the case that motif score changes and physical differences in binding affinities are not perfectly correlated, reflecting the fact that sequence motifs are an imperfect model of biophysical binding preferences [ 30].
Measuring TF binding affinities is not an easy task experimentally; however, it can be approached from the nucleotide preferences at each sequence position [20], e.g., position weight matrix (PWM).
We demonstrate that important aspects (defect position influence, differences between DNA/DNA, RNA/DNA and RNA/RNA hybridization, surface and bulk hybridization) about the impact of point defects on oligonucleotide duplex binding affinities are not yet understood.
No significant effect of peptides on anti-CCR5 binding was observed indicating that the peptides bind to an epitope distinct from the antibody-binding site or their binding affinity is not sufficient for effective competition with this particular antibody.
On the other hand, the antiviral activity of interferons on WISH cells seems to change in accordance to the binding affinity towards IFNAR1 only as long as the binding affinity is not beyond twofold of the wild-type.
Moreover, the binding responses were similar to values obtained for the interacting proteins, indicating that the binding affinity was not affected by the fusion.
The binding affinity of JEV SA14 and SA14-14-2 to thostost cells is similar (Fig. 2B), so the binding affinity is not the main cause of JEV SA14-14-2 neurovirulence attenuation.
