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From the validation results it was found that GH (Goodness of Hit) scores for the selected ligand based and structure based pharmacophore models were 0.89 and 0.97, respectively, which indicate that the quality of the pharmacophore models are acceptable as GH value is >0.7.
Unlike commercial SPR sensors which operate at one λSPR, the new device can be used for sensitivity analysis at selected λSPR in the range 550 750 nm, offering the possibility to identify the highest sensitivity λSPR in regard to the spectral changes of the selected ligand.
The selected ligand's row is highlighted orange.
positioning the selected ligand conformation into the binding site, and (4) rigid body energy minimization of the candidate ligand pose/conformation using the DockScore energy function and updating the saved list of ligands with the candidate pose.
Correlation coefficient analysis was performed between energy scores calculated for all the selected ligand molecules, log P value, and molecular weight (Table 1).
Molegro Virtual Docker docked the selected ligand SAM with both the hypothetical protein and the reference protein (3P2 K: D) with grid lines X: 21.84; Y: 10.96; Z: −7.07 and X: 21.87; Y: 10.94; Z: −7.12, respectively.
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Hence, the selected ligands only come from HET records excluding MODRES ones.
Hence, the present study is interested to evaluate the interaction of the selected ligands with the breast cancer target receptor.
The selected ligands range from hydrocarbons having isolated π-bonds and aromatic rings to conjugated polyarenes with planar or curved unsaturated carbon surfaces.
Further, in silico point mutation of BAX-Lys21 to Glu21 resulted in structural change in BAX and showed reduced binding energy and hydrogen bond interactions of the selected ligands.
The selected ligands, cholesterol, 25-hydroxycholesterol, 5-cholesten-3β-ol-7-one and probucol bind to the predicted active site cavity of Mce4A, and complexes remain stable during entire simulation of 100 ns.
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Justyna Jupowicz-Kozak
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