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Recent validation studies have highlighted the poor performance of currently used scoring functions in estimating binding affinity and hence in ranking large datasets of docked ligands.
Moreover, we found that the TEM8 L56A mutant strikingly increased the PA binding affinity and hence can be used as a good decoy antitoxin.
Multivalent versions of these peptidomimetics have been created with the goal of improving integrin binding affinity and, hence, tumor uptake [44], [45].
Here, imperfections in the IR sequence decrease binding affinity, and hence are important for precise regulatory control (Sadler et al. 1983).
Due to the poor performance of current scoring functions in estimating binding affinity and hence in ranking docked ligands, it is recognized that compound selection based on calculated scores is not sufficient and visual inspection is often necessary.
However, this rather modest potency boost after gaining two additional major hDAAO interactions suggest that the path through the subpocket by compound 3 is less favourable than for compound 2, or that some of the interactions found in compound 2 but not in compound 3 (see Figure 3B for two examples) are key drivers of binding affinity and, hence, inhibitory potency.
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Reoccupation of the S1 site by a new substrate is thought to reactivate the InsP6-binding affinity and hence the proteolytic activity of MARTX-CPD.
Hence, the lack of oxygens in the structure of PCBs can be correlated to their weaker binding affinity (and consequently their lower molar toxicity).
Even so, the low affinity binders can undergo in vitro affinity maturation to improve their binding affinity and specificity5,39,42.
Hence deprotonation, amidation, acetylation, benzoylation, benzylation, and addition of phenyl, deoxyglucose and glucose fragments were performed to increase the binding affinity and to prevent its rapid degradation.
In vitro binding affinity and efficacy analysis demonstrated that the bivalent isoform had the highest binding affinity and in vitro efficacy.
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