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Since ChIP-DNA fragments are equally likely to be sequenced from both ends, the tag density around a true binding site should show a bimodal enrichment pattern, with forward strand tags enriched upstream of binding sites and reverse strand tags enriched downstream of binding sites [ 10, 11, 35, 37].
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Adenine, with its two metal binding sites, should show the best affinity, whereas thymine, with no strong metal binding sites, should show little or no affinity.
At a fixed concentration of Fluoro-probe, inhibithat that bind to the FPP binding site should compete with Fluoro-probe for binding to UPPS and show a competition profile similar to that illustrated in Figure 3A.
Its binding site should be well characterized.
This secondary DNA binding site should accommodate approximately 5 nt of the translocating strand.
Molecules designed to occupy the UDP-Ara4N binding site should provide specificity for bacterial targets.
The DnaA binding site in these two species differs because of one nucleotide, suggesting that the binding site should also be very conserved in alpha proteobacteria.
Important considerations for designing metal-binding sites are that packing interactions in the binding site should be carefully considered to avoid costly reorganization energies and binding to the unfolded stable should be destabilized (negative design).
Sterical demand close to the phosphate binding sites should inhibit coordination to the nucleobases.
Acknowledging that similar binding sites should recognize similar ligands, a structure-based alternative to docking, is the 3-D comparison of protein-ligand binding sites [37].
Intuitively, constitutive binding sites should be biologically functional.
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