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The link between determining binding specificity and finding sites where the transcription factor is likely to bind is the way in which binding specificity is represented.
If the unidirectional cluster growth to the pointed-end is driven by the shortened helical pitch on the pointed-end side of the cluster, the new molecule is likely to bind any of the vacant binding sites in the supertwisted, apparently, bare zone on the pointed-end side of the cluster.
A binding pocket that is likely to bind a ligand will have an Sscore greater than 0.8 and a Dscore greater than 0.83 [44] 44].
The authors argue that the C-terminal domain of unc-116 is likely to bind microtubules based on sequence similarity (but not identity) of the MT binding domain to homologs, but whether the C. elegans sequence binds to MTs is not known.
The N-terminal domain, being related to the ribosomal proteins L30 and L7Ae, is likely to bind RNA.
Hg II) was used as the probe, which is likely to bind to mesoporous silica spheres functionalized with either amine or thiol groups.
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All of these compounds are likely to bind in an inter-subunit binding cavity at the top of the TMD which imposes an upper size limit upon them (Stevens et al., 2005; Nury et al., 2011).
These inhibitors do not block the N-terminal domain's ATP-binding site, and thus are likely to bind at the C-terminal domain.
Hence, these nine different descriptors are suitable for formulating a scoring function that can differentiate between small molecules that are likely to bind kinases (actives that have kinase-likeness) and those that are not.
One way to solve this question is the use of enantiomeric substances, as enantiomers have the exact same physical properties, but are likely to bind with different affinities to proteinaceous and thus chiral binding sites.
CTCF is a sequence-specific Zinc-Finger DNA binding protein [28], and we thought it was likely to bind the rDNA directly.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com