Sentence examples for binding sites are typically from inspiring English sources
Unfortunately, these binding sites are typically short and degenerate, posing a significant statistical challenge: many more matches to known TF motifs occur in the genome than are actually functional.
This is to be expected, as ligand binding sites are typically the most important part of a structure model, and much attention is paid to ensure that the model is correct in that area.
Transcription factor binding sites are typically linked to their direct target genes.
The reported MHC binding sites are typically identified using truncation, substitution, or mutations in a base peptide [36].
Second, since transcription factor binding sites are typically degenerate, an information-based (as opposed to string-based) search methodology will be most successful at finding universally shared regulatory motifs.
As these regulatory DNA binding sites are typically short (5 20 bp), knowing the exact location of nucleosomes along the DNA is crucial for understanding the transcriptional blueprints embedded in the DNA (e.g. Narlikar et al., 2007).
These potential binding sites were typically found based on the analysis of the reported x-ray crystallography or NMR data on structural characterization of a fragment of a target protein bound to its partner(s).
DOI: http://dx.doi.org/10.7554/eLife.04530.012 Dali binding sites were typically limited to less than 1 kb in length and were distributed across the genome with no apparent chromosomal biases other than a depletion on the X chromosome which may reflect the inactivation of one X chromosome copy in these female N2A cells.
NR-binding sites are typically composed of a pair of 5 6 base-pair-long DNA sequences (two half-sites) which are often separated by a spacer of 1 6 bases of length (Bain et al. 2007; Urquhart et al. 2007).
Naturally, the noninhibitory NMR hits might bind elsewhere on the enzyme, but trying to anticipate this would be outside of the normal docking protocol, where a key binding site is typically targeted.
Because the number of observed evolutionary differences in any particular binding site is typically small, I make the assumption that each DNA difference in a transcription factor binding site occurs independently, and presence of a single change has no effect on the probability of other changes.
