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In practice we find that the three ensembles have similar average structures
Three simulations of the 1-ligand EGFR homodimer, generated average structures with a root-mean-squared deviation of 1.9 4.8 Å from one another, as measured based on the Cα atoms of domains I III.
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In the intermediate temperature range the molecules are displaced from their room temperature positions in such a way as to give an average structure with Cmc21 symmetry.
With water molecules stripped off, the average structure with the shortest distance was then energy minimized (performing 50 cycles of steepest-descent minimization and then 150 cycles of conjugate-gradient minimization using a dielectric constant of 80.0).
10 initial references were produces from the average structure with an addition of low, 10% Gaussian noise.
This difference in the conformation of Tyr may be a result of the hydrolysis because we are comparing the covalent-orlistat in the simulated average structure with the hydrolyzed orlistat in the crystal structure.
The resulting ensemble and average structures agreed well with the NMR data, where the experimental restraints had low root-mean-square deviations (rmsds) (Table 1).
This is confirmed by the average structure model with (1 b) cell dimensions as for triplite and F distribution conforming to the distributions in both the (1 b) and (2 b) types.
We hypothesized that forests with equivalent average structures (e.g., basal area) would have higher stand-level seedling growth and survival in aggregated retention versus dispersed retention stands.
The distances between the trimethylene protons and X N1H, NH in the average structure also agree with the NOEs of the trimethylene with X N1H and NH.
An average structure was obtained with Weatsheaf (25).
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