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The calculated root mean square deviation between calculated and experimental pH stability optima is 0.78 for the dataset of 19 enzymes, comparable with the value of 0.72 for the earlier work [ 31], and supporting the use of Debye-Hückel modelling in this study.
We also have calculated root mean square (RMS) of fingers and its variation with time.
The calculated root mean square distances (RMSD) between HAVCR1 and CD4, CXADR, and HAVCR2 were 2.3, 1.9, and 1.3, respectively [46], [47], [48], [49], [50].
We investigated the stability of both forms of M2-1 using classical molecular dynamics simulations (MDS), and calculated root mean square fluctuations (RMSF) along the trajectories.
Lastly, the following goodness of fit indicators were calculated: Root mean square error of approximation (RMSEA), goodness of fit index (GFI), adjusted goodness of fit index (AGFI), comparative fit index (CGI), and normalized fit index (NFI).
We run a 50 ns simulation at the same pH at which crystals were grown and calculated root mean square fluctuation (RMSF) values as a measure of flexibility per residue.
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For the quantitative analysis of the model improvement, we calculated Root Mean Squared Error (RMSE) and Mean Absolute Error (MAE) for each method with direct metering data.
To estimate the level of regional BOLD signal fluctuation we calculated root mean squares (RMS) of percentage signal change for the PCC (where our DMN calculations originate) and the Left precentral gyrus (BA4) where we found the highest statistical peak for the comparison of moderate sedation vs. awake states (see Table S3 and Figure S1).
Utilizing the MD simulation data, we examined the flexibility of the MHC molecule and the peptide epitope by calculating root mean square fluctuation (RMSF) of the peptide backbone atoms and the backbone atoms of MHC residues interacting with peptide (within 5 Å of the peptide).
First we survey the stability of all atoms performed by using the GROMACS 4.5.5 software though the commands of g_rms and g_gyrate to calculate root mean square deviation (RMSD) and radius of gyration (Rg), respectively.
All EMG data are calculated root-mean-square (RMS) with 500 ms section.
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