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Cells can form a cluster of many monovalent receptors on the cell surface [ 32], and particularly multimeric ligands with a spacer between the binding moieties could span the required distance between binding sites and could then bind multiple receptors simultaneously.
Using homology modeling and ligand docking, the present study analyzes the similarities and differences between binding sites, and between extracellular loops of the three subtypes of α2-ARs.
The decreasing trend of q e value with the increasing adsorbent dosages may result from the electrostatic interactions, interference between binding sites, and reduced mixing for higher densities at higher dosages of adsorbent (Fourest and Roux 1992; Montanher et al. 2005).
However, the precise nature of the relationship between binding sites and Hill coefficients remains a matter for discussion [69].
Gaussian mixture modeling of distances between binding sites and motifs was performed with R package mclust (Fraley & Raftery, 2002).
Ma's report shows that several structurally conserved residues could be used to distinguish between binding sites and general exposed surface; for instance, conservation of Trp, Phe, and Met residues on the protein surface was shown to be associated with a higher likelihood of formation of a binding site [8].
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Although the KAc sites of BET proteins are highly conserved (Supplementary Table S4), subtle structural differences may influence shape complementarity between binding site and ligand.
For all entities, the number of binding sites and angles between binding sites must be specified, and an entity binding to a previously free binding site of an entity with an already occupied site will always be placed such that the relative angle matches the specification, independent of its previous position, i.e., the angle from which it collided.
Understanding the intermolecular interactions between binding sites of analytes and recognition sites of imprinted cavities that allow molecular recognition is essential for proper MIP design.
It should also be noted that although there are some structural similarities between binding sites of CERT and I2PP2A/SET to ceramide, there are also major differences.
Additionally, Gene Set Enrichment Analysis found strong correlation between HIF binding sites and up-regulation of genes, whilst there was no correlation between down-regulated genes [ 33].
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