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A compound that acts as an estrogen receptor ligand in mammals will often also bind to these receptors of fish, and available evidence suggests that binding affinities can be comparable among species (Tollefsen et al. 2002; Urushitani et al. 2003; Wilson et al. 2004).
The relative binding affinities can be simultaneously determined.
Many approaches for computing binding affinities can be classified as linear interaction energy (LIE) models as they rely on some type of linear fit of computed interaction energies between ligand and protein.
These binding sites may have low sequence specificities, but their binding affinities can be complemented by high structure specificities.
The binding affinities can be compared to the affinity constants determined for MBP from the association and dissociation rates (kon/ koff) and measured with stopped-flow fluorescence spectroscopy.
This approach is based on the well established 'glycoside cluster effect', in which binding affinities can be dramatically increased by a clustering of both lectin binding sites and carbohydrate recognition units on the surface of cells or tissues [ 33].
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DNA binding modes and binding affinity can be modulated by ligand design.
We show that type II binding can have a profound influence on binding affinity for CYP3A4, and the difference in binding affinity can be as high as 1200-fold.
The computational findings were then verified by using fluorescence analysis; it is indicated that the halogen type and substitution position play critical role in the interaction strength of halogen bonds, and thus the PDZ5 peptide binding affinity can be improved considerably by optimizing their combination.
Based on these, energetically favorable and unfavorable contributions to the binding affinity can be assessed on an atomic level.
With the formation of ligand protein complex, binding affinity can be evaluated by monitoring the heat that quantitatively occurs in the release and absorption of the binding process [158, 159].
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