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Their predicted binding conformation within the large cavity of ABCB1 is yet to be determined.
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We used docking simulations to calculate their lowest-energy binding conformations within the thyroxine binding sites of human TTR, thereby providing corroborating evidence for their high-affinity binding, and insight into potential binding orientations.
In summary, these data suggest that the secondary low-affinity conformation of the β1-adrenoceptor may be a consequence of negative cooperative interactions between 2 orthosteric binding conformations within a β1-adrenoceptor homodimer.
Redocking of the peptide inhibitor (present within the active site of retrieved crystal structure of caspase-3) was performed to acquire and validate the size, center of the coordinate grid, and ligand binding conformation in the binding pocket.
Additionally, a docking model predicted the binding conformation of WHI-P154 within the transmembrane region of homology-modeled human ABCG2 transporter.
b The binding conformation of compound A1 in the active site of pancreatic lipase.
Active site was defined as the area within 10 Å from Lys340. Figure 5 shows the predicted binding conformation of inhibitor 9 in the active site of PBP2x 5204.
The active site was defined as the area within 10 Å from Lys406. Figure 4 shows the predicted binding conformation of inhibitor 1 in the active site of PBP2a.
Clearly, the binding conformation of DB00631 was impacted by the co-binding peptide.
Systematic search generates all possible ligand binding conformations by exploring the whole conformational space.
Figure 3 shows the binding conformation of orlistat (left) and vibralactone (right) in the active site.
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