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Although this study could not find the significant difference between medial and lateral parts of the thalamus, D3 binding sites are relatively abundant and especially tend to be concentrated along the midline in the thalamus, while D2 binding sites are more homogeneously distributed [24], [27].
Such binding sites are relatively short segments of DNA, normally 5 to 25 nucleotides long.
This reflects the fact that multiple, large binding sites are relatively tolerant of a small number of mutations.
Since these two binding sites are relatively close and positioned at the same side of the molecular surface, we speculated that binding at one site may interfere with binding at the other site.
Compared to the number of the NF-κB binding sites found in the promoter region of genes encoding the members of NF-κB and IRF family, the IRF binding sites are relatively poorly represented.
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Indeed, the DNA methylation level at the 12th position of CTCF-A binding sites was relatively high compared to other CpG sites (Additional file 11: Figure S6).
For example, FOXA2 is active in the liver [ 21], pancreas [ 22] and potentially hair follicles [ 23], and FOXA2 binding sites were relatively hypomethylated in these tissues.
For example, Abf1 and Reb1 show the highest linker ratios, implicating that the chromatin structure in their binding sites is relatively open.
On the other side of the spectrum, when networks are not sparse, and the spontaneous gain rate of binding sites is relatively equivalent to their loss rate, selecting on a specific pathway function does not affect regulatory complexity.
Since the number of binding sites used to construct the preliminary profile of CRP binding sites was relatively small (for the reason, see the Results section), in order to minimize possible bias of binding site sampling, we conducted a one-round iteration to obtain a more representative profile of the CRP binding sites.
In the other cases, where conformational changes in the binding site are relatively small (RMSDmax.<3 Å), the druggability scores vary only slightly, including for the cases where ligand-free structures were available (Alr2, CDK2, DHFR and thrombin).
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