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Kinetic analysis suggests competitive inhibition and the binding model of these compounds can be rationalized using molecular modelling studies.
Although the docking results have not been verified by site-directed mutagenesis or co-crystal complex of vardanafil-ABCB1 and tadalafil-ABCB1, in the interim, the binding model of these ABCB1 inhibitors may serve as a guide for further lead optimization studies.
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To demonstrate that dense network of distance constraints benefits the molecular modeling, we used all the generated XL distance constraint for local perturbation modeling to create a comprehensive binding model of the M1 protein on the bacterial surface (Fig. 4b).
The binding model of this particular scaffold is similar to that of Flavopiridol (Figure 1A), an experimental drug currently in clinic trials, with an additional hydrogen bond between the N-H group of the lactam and carbonyl group of Leu83.
(B ) Heatmap showing interdependency between bases in the binding model of the Runt family TF lz.
Migration assay results for the antagonistic compounds 1 and 2 and a binding model of the chimeras to CXCR4.
(4) The heat capacity changes (Δ C p °) associated with the binding of the different SAHA analogues to HDAC8 cannot be rationalized in view of the classical hydrophobic binding model of the enzyme ligand complexes.
The 2D and 3D binding models of the complex 19a/11β-HSD1 were generated using docking simulations.
The binding models of the investigated antagonists indicate the mechanism of binding of the studied compounds to the CCR5 obviously.
We constructed binding models of the TFs regulating pattern formation in the early embryonic development of D. melanogaster (Mel) and applied them to the genome of D. pseudoobscura (Pse).
These similarities allow us to construct a binding model of 5′ flap DNA with hFAN1 characterized by extensive interactions with all three domains in a sharply bent DNA conformation.
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