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The docking was considered valid, only if the reference root mean square deviation (RMSD) was equal to or less than 2 Å [ 25].
Docking was considered acceptable if the average RMSD value of the docking poses was less than a given threshold of 2.0 Å from the crystal pose.
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The structure-based molecular docking is considered a suitable approach for the development of new drugs, since this approach is targeted to specific protein and specific pathway [47].
The average donor and acceptor fluorescence intensities measured before docking were considered as the background fluorescence for each fusion event and subtracted uniformly from the fluorescence signals.
Docking is considered the first necessary intermediate maturation step before either LDCVs or SVs gain fusion-competence and release their neurotransmitters.
Molecular docking is considered to be an important tool to investigate the mode of interaction of ligand with the target and to elucidate the underlying binding mechanism.
In recent years, Surflex-Dock are considered as the most accurate in terms of docking and it is clearly superior to other methods within the set of cases for which comparative data are available, with roughly double the screening enrichment performance63.
The molecular docking approach was considered for pose analysis and scoring; in addition ligand based strategies were employed for pharmacophore mapping and similarity search.
For the hDATdDAT model, only one docking pose was considered in which the positioning of the C-terminus closely followed that in the dDAT X-ray structure, and the N-terminus was docked so as not to contact any residue in the TM bundle.
This was a commercial dock, and was considered by XX Bomber Command planners to be "the only suitable primary target free of stipulations left in this theatre".
Since the magnitude of the objective function differs entry by entry, the ratio of the optimized objective function of the model to that of the native complex, called the "relative docking-score", was considered, where the objective functions of the native complexes were calculated in the same way as that in the sampling method.
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