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In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer.
The fact that some BORIS isoproteins can bind the same targets as CTCF (Fig. 7 and Fig. 8) prompted us to determine if the functional consequence of binding to a given target would be comparable for both CTCF and BORIS isoproteins.
In addition, the absence of binding to a given peptide may provide data on inhibitory effects of specific residues.
CoMFA first aligns the ligands capable of binding to a given target, and then measure field intensities around the aligned ligands by different atom probes (force field-based).
Here, we demonstrate a high-throughput methodology allowing rapid identification of the proteins binding to a given human RNA molecule using a protein microarray containing ~9,400 human recombinant proteins spotted in duplicate.
Moreover, several groups including ours have shown previously that several peptides that do not fit the consensus sequence for peptides binding to a given MHC molecule can activate T cells restricted to that MHC molecule very efficiently [ 33- 36].
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The density of TF-binding to a given segment of chromosomes was estimated by quantifying the number of protein-specific binding events per 1-Mb and 1-kb consecutive segments of selected human chromosomes and plotting the resulting binding site density distributions for visualization.
Predictions of binding affinity to a given substrate are based on similarities in binding-site signature.
As has been experimentally documented [ 17- 19], the cohesin type (i.e., type I or type II cohesin) does not necessarily indicate its binding specificity to a given dockerin.
Typical Nanobody characteristics (such as small size, single-domain nature, and robust folding) make formatting and the construction of second-generation libraries based on a previously selected Nanobody more straightforward [ 14], which can be exploited to optimize binding characteristics to a given antigen more efficiently.
For the weight matrices/energy matrices used in the study, see Additional file 1, Additional file 2, Additional file 3 and Additional file 4. The energy matrices constructed using each of the methods allows one to assign an estimated binding energy to a given site.
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