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In both of the recombinant polypeptides, DNA binding specificity is shown to track with the basic region.
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Similar binding specificity was shown for the parent antibody V5B2 [13].
The differences discovered between human and murine TAP binding specificity were shown to correlate with differences in the ability to predict epitope recognition in murine hosts.
PFM prediction examples for several TFs with unknown DNA-binding specificity are shown in Figure 7 (a).
This figure clearly shows that binding specificity is primarily determined by the structural family of the TF.
For example, NMR analysis of the SH2 domain of Inducible Tec Kinase (Itk) showed that its binding specificity is modulated by cis-trans isomerization of a single proline [ 4].
This is a reasonable approximation, as molecular binding models describing the interactions between transcription factors and DNA have shown that binding energies are approximately additive between bases [9] (in other words, interaction of binding specificity is negligible).
This redirects LRH-1 binding as predicted and showed that, in this case, evolutionary importance and binding specificity are coupled sufficiently strongly for the Evolutionary Trace to guide the computational design of DNA binding specificity.
Actin binding specificity was demonstrated by competitive binding experiments and comparative staining of well-known structures.
Details of binding specificity are provided in SI Figures S5 S7.
Specificity of binding can be shown in terms of reproducibility of the docked conformation of the compounds.
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