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Although fast and accurate computational prediction of binding affinities for an arbitrary molecule is still beyond the limits of current methods, the docking and screening procedures can select small sets of likely lead candidates from large libraries of either commercially or synthetically available compounds.
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Using this CETSA HT approach we can derive apparent binding affinities for a range of AR antagonists, which represent an intracellular measure of antagonist-receptor Ki performed for the first time in a label-free, disease-relevant context.
Available experimental binding affinities for a small number of the tested compounds show very good agreement with the calculated energies and provide the rational approach for design of Gal-3 ligands with even higher affinity.
We used the function to blindly and successfully predict binding affinities for a diverse test set of 31 wild-type protein protein and protein peptide complexes (R2 = 0.79, rmsd = 1.2 kcal mol− 1).
Generally, the task of ligand-based VS is to output a ranking list of a set of molecules in terms of their binding affinities for a given drug target, so that the top-k molecules can be further examined through in-vivo or in-vitro test.
Neither the 8-phenoxymethylcaffeine nor the 8-[ phenylsulfanyl)methyl]caffeine derivatives exhibited high binding affinities for MAO-A.
Comparison of the binding affinities for lipid A and daunorubicin when the two compounds were presented to the protein in an ordered fashion indicated that the two binding sites engage in complex interactions with each other.
IR binding affinities for IR-A in membranes of human IM-9 lymphocytes of all the prepared analogues are listed in Table 1, with the corresponding binding curves provided in Figure S2 of the Supporting Information.
The immunoglobulin binding affinity for an encountered antigen is dynamically optimized in the process of affinity maturation that takes place in germinal centers.
Strep-tag II has a strong binding affinity for an engineered streptavidin derivative called Strep-Tactin, which enables fast and simple one-step purification [34].
Conversely, Bub3 did not show any binding affinity for an unrelated phospho-peptide.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com