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Exact(7)
However, as previously reported, it may be challenging to identify the ligand binding site when the binding energies of the different positions are similar [35].
A subsequence of the length of the PWM is declared a binding site when the p-value of its PWM score is less than or equal to a preset threshold value.
A CTCF binding site was considered a constitutive binding site when the same motif site was present in more than 90% of the 55 cell lines.
However, the C- terminal exhibited much higher affinity for a cooperatively influenced binding site (for a Ca2+ binding site when the neighbouring site is occupied).
Rotation of the side chains of Y108 and F253 was found to allow opening of the binding site when the substrate exited.
The Δ Fmax for lipid A quenching also increased 2-fold when daunorubicin was bound first, indicating that conformational changes take place at the lipid A binding site when the drug-binding site is occupied.
Similar(52)
However, computational methods for locating constitutive binding sites when the protein does not bind directly to DNA are still lacking.
Two proteins are likely to have different binding sites when the algorithm effectively distinguishes between their binding areas.
42 This observation is attributed to steric hindrance between neighboring binding sites when the assembly is highly packed.
This analysis provided estimates for the affinity constants for ABA-X-BY630, XAC, and NECA and cooperativity factors between A3-AR binding sites when the homodimer was simultaneously occupied by 2 ligands.
DROMPA identifies protein-binding sites when the peaks are sharp (approximately 1 kbp, e.g., transcriptional factor binding sites) and when they are broad (approximately 1 Mbp, e.g., modified histone binding sites, such as H3K27me3 and H3K36me3), as a consequence of the simple peak-calling strategy used.
Related(14)
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