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Because we lack logP measurements for many of our molecules we use a Crippen's model of logP.
Taking into account screening effects between electrodes and central molecules, we use 10-unit cell's length as scattering regions, and 2 units as electrodes to perform transport calculation.
In order to calculate the pairwise similarity between two molecules we use Tanimoto similarity scores, [26] which we transform into probabilities (p-values) using an appropriate kernel function.
In order to consider synthetic accessibility of in silico generated molecules, we use our inhouse libraries of drug-like and chemically feasible molecules for the in silico fragment generation.
To capture biologically meaningful sets of interacting molecules, we use experimentally defined pathways as spatial/temporal units of molecular activity.
To illustrate how force measurements of molecules are done to obtain the parameters that define the mechanical properties of molecules, we use single molecule force studies of a protein with repeated units.
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To evaluate the neuroprotective activity of these molecules, we used midbrain cultures and various experimental conditions that promote dopaminergic cell loss.
However, as the protein files provided by the sc-PDB do not contain water molecules, we used the corresponding original files from the PDB instead.
The dot-dot distance, l, in these molecules is between 0.5 to 0.8 Å. Bistability and electron localizability of these molecules have been studied in [3, 46, 49]. Figure 4 Geometry of the molecules we used in our calculations.
To analyze the expression of cell surface molecules we used monospecific antibodies, fluorochrome dyes and flow cytometry.
To achieve a uniform expression of the transfected cDNA and to make sure that the transfected MHCII subunits are integrated into endogenous MHCII-Ii complexes and introduced into the biosynthetic route of MHCII molecules, we used stably transfected cell lines.
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