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Suppose that there are m repeated binding sites to which T binds and suppose that each site has the same association constant.
The site modification (uppercase) 'P' is reserved for indicating the phosphorylation of binding sites to which effectors bind in other layers.
The site modification (uppercase) 'P' is reserved for indicating the phosphorylation of binding sites to which the effectors bind in other layers.
The sole difference is that the phosphorylation of binding sites to which the effectors bind in other layers has to be indicated by a site modification (uppercase) 'P'.
Using this approach, it has been found that BINDSURF predicts accurately and at an unprecedenteded speed the binding sites to which different ligands bind to the same protein in known cases that were problematic to other docking methods.
To investigate the relevance of these interactions for the ESC transcriptional network, we tested the effect of acute Oct4 depletion by 12 hr doxycycline treatment, on the recruitment of Dax1, Tcfcp2l1, and Esrrb to a number of genomic binding sites to which Oct4 also binds (Chen et al., 2008b; Kim et al., 2008).
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To indicate the phosphorylation of a binding site to which the effector binds in another layer, the site notation (uppercase) 'P' is used.
For a number of years, we have been pursuing novel inhibitors of DHPS that target the conserved and structured pterin-binding pocket with the goal of producing broad-spectrum drugs that are less prone to generating resistance than the flexible pABA binding site to which sulfonamide drugs bind.
Although it has not been possible to measure the levels of nikABCDE transcription as a function of cellular nickel concentration, in vitro studies suggest that NikR has a third type of metal binding site to which excess nickel ions bind, changing the dissociation constant of NikR for DNA from the nanomolar to picomolar range (1, 2).
Glycine substitution of this residue destroyed binding to this site, whereas notably, TtgR has a second "general" binding site to which phloretin and other drugs bind with lower affinity, which is not dependent upon charged residues (29).
The most conserved cluster of potential binding sites for HIV-1 protease corresponds to the protease catalytic binding site to which many compounds are known to bind.
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