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ChIP-chip peak calling: Oftentimes oligo intensities will vary within a binding site due to lack of sensitivity in hybridization.
It is worth noting that this rate limiting step is not necessarily caused by the diffusion and/or binding of the protons inside ZmSUT1 but could be influenced by the accessibility of the proton binding site due to conformational changes of the transporter.
In contrast, a phosphate at the 6-inositol position is unlikely to be tolerated without reorganization of the binding site due to a steric clash with S35.
Permanent farnesylation of progerin could mask the loss of this actin binding site due to the tight interaction between the progerin-farnesyl group and nuclear envelope [ 52- 54] and/or gained binding partners by progerin mutant [ 2].
Through comparison to the homologues USP4 and USP15, we have highlighted several novel features in USP11 including: (i) the absence of a pronounced hydrophobic DUSP pocket previously predicted to constitute a protein binding site due to sequence variations in the N-terminal helix and surrounding residues.
This allows us to model the uncertainty in actual binding site location–experimental methods may not precisely locate a binding site, and may include a region that is larger than the true binding site due to limitations of budget and experimental procedures.
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Such behavior can be attributed to saturation of the dye binding sites due to particulate interaction such as aggregation (Aksakal and Ucun 2010).
Since lectins bind to specific carbohydrate residues on the cell surface, the decrease in staining reflects the loss of these binding sites due to radiation-induced membrane damage.
In both cases, the binding site is not inside the channel cavity and thus there are six equivalent binding sites due to the six-fold symmetry of the p7 channel.
This increase likely is reflective of the increase in the number of rhBMP-2 binding sites due to multivalency in the presence of the three heparan sulfate chains in PlnD1 (Jha et al. 2009).
We have devised a strategy of using engineered viruses to deliver decoy hyper binding sites for HMGA1 to the nucleus of cancer cells with the goal of sequestering excess HMGA1 at the decoy hyper binding sites due to binding competition.
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