Compounds that showed double binding in crystal structures (13, 16, and 17) had their ITCs fitted using a one-site binding model, as this gave the best curve fitting, suggesting the second binder remains relatively weak.
The BiasAway GC nucleotide background and HOMER generated backgrounds performed comparably for most measures, with the exception that the BiasAway background resulted in an 11 percentage point improvement for the inclusion of the ChIP'd TF binding model as one of the top 5 over-represented.
We determined experimental KD values using a binding model as described in the Methods section of 5.5 ± 1.3 µM for HA, 5.5 ± 1.0 µM for DS, 4.8 ± 0.7 µM for CS4 and 1.4 ± 0.4 µM for CS6 for the GAG hexasaccharides.
The experimental data were analyzed using the single-site binding model as described previously by Wiseman et al., which yielded the magnitudes of the stoichiometry (n), the association constant (Ka), and the standard enthalpy change (Δ H °) for the binding of ligands to HDAC8.
The ensemble of data was globally fit to the nonspecific finite lattice DNA binding model as described in Experimental Procedures (eq 1c), which yields an excellent fit to all of the data sets well.
The results were analysed assuming a one-to-one binding model as previously described [27].
The relationship between free and total cefazolin concentrations was best described using a constant binding model as follows: (7) C total = C free f u, where Ctotal represents the total drug concentration and f u represents the (estimated) fraction of free drug.
We propose a two-metal binding model as a potential mechanism of chelating inhibitors against HIV integrase (HIV IN) represented by 2-hydroxy-3-heteroaryl acrylic acids (HHAAs).
The relationship between FRET efficiency and A/D ratio was modeled with a simple 1∶1 ligand binding model as described before [33], [34].
Hitherto, such atypical kinetic behavior was attributed to a mechanistic scheme involving alternate substrate binding site(s) near the CYP enzyme's active site[11] [14], which is a two-site binding model, as shown in Figure 1.
