Sentence examples for root mean squared deviation (RMSD) from inspiring English sources

Therefore in order to assess the impact of these features on the template structures, the root mean squared deviation (RMSD) was calculated between each TMH of each of the 5 templates; Table 6 shows a sample of these results (TMH2), with the remaining TMH RMSDs being found in Text S3).

A decoy set for a given protein typically includes the experimental structure (as determined by nuclear magnetic resonance or X-ray crystallography), so that the quality of each decoy can be verified objectively using measures such as the root mean squared deviation (RMSD) from the experimental structure or the Global Distance Test (Zemla, 2003).

b Time-dependence of root mean squared deviation (RMSD) of the ligand measured from its reference pose.

Similarity of conformers toward the crystal-pose was quantified as the best achievable root mean squared deviation (RMSD, heavy atoms only).

Fig. 5 Structural fits quantified as root mean squared deviation (RMSD) with values given in Å. Ligand conformations after Shaker (grey) compared to the crystallographic references (red sticks).

To monitor the conformational changes during the simulations, the root mean squared deviation (RMSD) between the initial coordinates of the backbone atoms of the proteins and the coordinates along the MD simulations was computed for every snapshot.

Note that the statistical errors of RMSF values generated by CABS-flex are reflected in root mean squared deviations (RMSD) between RMSF profile data (Fig. 2B).

Then 1500 steps of a steepest descent energy minimization followed by 5000 steps of adopted basis Newton-Raphson minimization (or until the root mean squared deviation [RMSD] was less than 0.001 kcal/mol Ǻ) was conducted.

The mean average deviation (MAD) and root mean square deviation (RMSD) over one gait cycle are reported.

The "root mean squared deviation", or RMSD, method is restricted to binary trees [ 18], see Additional File 4 for full set of results.

A detrended fluctuation analysis (DFA) showed that the root mean squared deviation from the detrended time series increases as a power of the window width (Fig. 6b).