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To distinguish between these possibilities, we used a single-molecule technique for directly observing Ago2-target binding events that we recently developed (Chandradoss et al., 2015).
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In the third and last set of RW simulations, we studied binding events that were registered during a transient response in the cleft.
We observed transient RNAP binding events that lasted between 0.08 and 8 s, and were promoter-specific.
Once it is possible to distinguish true binding events that are functional from those that are non-functional, we will also be able to investigate the molecular factors distinguishing one from the other.
For SMAP query structures that were protein complexes containing multiple subunits, if the predicted ligand binding site included residues from distinct subunits, we flagged these as possible ligand binding events that could prevent or disrupt complex formation and therefore function.
We find a small but reproducible set of CTCF binding events that overlap with both the nuclear receptor, estrogen receptor, and the forkhead protein FOXA1.
Also the effective concentrations of ligands in these methods are very high, and consequently they can detect weak binding events that may not be physiologically relevant.
Taken together, it appears that E2F4 has a substantial number of binding events that are entirely dispensable for proper transcription of downstream genes, despite the well-characterized role it plays in cell cycle control.
By measuring subtle changes in the NMR parameters of the ligand (such as chemical shifts and relaxation times) one can probe binding events that occur at the µM to mM concentration range due to the fast exchange between the bound conformation and free form of the ligand.
Dynamic binding events that require the fewest additional cofactors are the ones most likely to be functional.
There were 98,561 annotated interactions pertaining to phosphorylation, gene expression and physical binding events that mapped to siRNA targeted genes.
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