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We consider the binding of the repressor, nuclear Mig1p, and Gal4p, to the respective binding sites as reversible stochastic reactions.
As an example, consider the binding of a molecule R with n sites and a molecule S with k sites.
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Considering the binding of α-subunits [ 25], the holoenzyme footprint can be extended upstream to position -60.
This suggests that if one considers the binding of GroEL with substrate protein candidates, it does so with the non-native form of the protein i.e. only one chain among two should be considered for the calculation of stability.
It is important to consider the binding strength of these interactions to help us construct more biologically relevant protein interaction networks that consider cellular context and competition between potential binders.
Considering the binding energy of Ag 3d3/2 and Ag 3d5/2, the valence of Ag in the heterostructure can be identified to be +1.
To the best of our knowledge, this is the first sequence-based prediction of protein-binding nucleotides in RNA which considers the binding partner of RNA.
Considering the binding energy of bulk Au 4f 7/2 peak (typically at about 84.0 eV), there is a significant negative shift in binding energy (corresponding to electron gaining) for the Au NPs on TiO2.
In contrast, our method predicts the binding sites by considering the binding conformations of the query ligand.
Some 30%% of these so-called 'holes in the T-cell repertoire' can be explained by considering the binding stability of the peptide HLA complex [ 46].
Recently, evolutionary analyses of large sets of transcription factor binding sites have highlighted the importance of considering the binding affinity or strength of the binding sites for their appropriate transcription factor [ 10, 11, 13, 18].
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