Root mean square difference

Figure 7-3. Active site properties of CAII from SCC-DFTB/MM-GSBP simulations [91]. (a) The root mean square differences between the RMSFs calculated from GSBP simulations (WT-20 and WT-25 have an inner radius of 20 and 25 A respectively) and those from Ewald simulation, for atoms within a certain distance from the zinc, plotted as functions of distance from the zinc ion that die center of die sphere in GSBP simulations is the position of the zinc ion in the starting (crystal) structure, (b) The diffusion constant for TIP3P water molecules as a function of the distance from the zinc ion in different simulations...

Probability distributions have been measured for Cd and Zn (1) and CdTe (15) for several nozzle dimensions and temperatures yielding effusion rates of 0.01-0.33 g/min. A representative distribution is shown in Figure 11. The curve drawn through the data points in Figure 11 illustrates agreement between the probability distribution F(< )), which was predicted by equations 25 and 26, and the experimental data. The root-mean-square difference between the experimental and predicted probability distribution values is 1-3% of the center line value. This agreement is as good as empirical fits described in the literature that use two or more adjustable parameters (16). 

FT-IR has been applied for determining the sucrose content of sugar cane juice [21]. In place of the more familiar transmission cell, an attenuated total reflectance (ATR) cell and clarified sugar cane juice were used to record FT-IR spectra from 800 to 1250 cm"1. In the spectra, significant wavenumbers (927.59, 997.02, 1054.87, 1116.51, and 1137.80 cm"1) have been identified for sucrose. The application of PCR has been proposed for the development of a calibration equation for sucrose content. PCR is basically a MLR applied to scores assessed by PCA. On the basis of FT-IR spectra and sucrose content, an accurate calibration equation could be obtained by the application of PCR. The root mean square difference between predicted FT-IR values and the actual values were 0.12 % (w/v) with a bias of -0.03 % (w/v). The accuracy of FT-IR for determining sugar cane sucrose is almost equal to that of NIR [25]. 

Finally, Table 5 shows statistics grouped by structure. For all of the structures, a root-mean-square difference between calculated and observed structural shifts of 0.25 to 0.35 ppm is found. Also shown are the slope and intercept of the best-fit line and the linear correlation coefficient for various portions of the total database. Statistics for all structures are not significantly different than those for the B-form DNA duplexes alone. Again, the best results are obtained for base protons and for the HI position on the sugar. 

The aim is to reduce the root mean square difference between the scores of the reference dataset and the transformed dataset ... 

The homology within the iLBP family has been compared at two different levels. Where the tertiary structure is known the root-mean-square difference in atomic positions can be calculated. Where only the primary structure is known, the levels of sequence identity between the proteins can be tabulated. This has been done systematically by algorithms that penalize for the introduction of gaps but use all the sequences simultaneously (Lipman et al., 1989), and this was followed by careful inspection and editing. In general, the two methods produced the same results. 

Root-Mean-Square Difference in Ca Coordinates for iLBPs of Known Crystal Structure... 

In the case of the fluorescein-binding variant FluA, crystals were obtained in the presence of the hgand at pH 8.1 with two FluA fluorescein complexes in the asymmetric unit, which were refined to a resolution of 2.0 A [52]. The two molecules were highly similar in structure, with a root mean square difference (rmsd) of 0.33 A for 173 mutually superimposed positions. The overall topology of the //-barrel with the a-hehx attached to it, both of which are characteristic features of the lipocahn architecture (see Section 8.2), was found to be conserved (Fig. 8.4). Both disulfide bonds of the BBP scaffold, one between Cys and fJys and one between Cys" and Cys, were also clearly visible. Upon superposition with the BBP crystal structure (molecule A from the Protein Data Base entry IBBP [32]), an rmsd of 1.2 A was calculated for 159 superimposed positions. 

Errors in difference syntheses are proportional to the root mean square difference of FpL —Fpl and hence are much less than those in the native electron density map... 

An expanded analysis of 68 quinazoline inhibitors of DHFR using this improved technique gave a RMS (root mean square) difference between observed and calculated fits of 1.33 kcal (experimental error about 1 kcal) (271). In addition to this correlation, the possibility of a variable binding mode of some inhibitors was noted and some suggestions were made to modify these quinazolines to make tighter binding ligands. 

No matter which approximations are made (or none), one can obtain a matrix Heff that is of the same dimension as the ligand field matrix. It is this matrix that one tries to approximate in AI LFT. Thus, in order to determine the LF parameters, one should form the root mean square difference ... 

Fig. 15.2-7 The shift match procedure can be divided into two steps. The identification of resonances of subsequent residues and the calculation of the root mean square difference (RMSD) in calculated and predicted chemical shifts, (a) Strips from the three-dimensional NMR spectra HNCOCACB and HNCACB. Through the matching of C and (T chemical shifts the neighboring amino acids can be concatenated to a "stretch . The positioning of this stretch onto the primary sequence, putative Ala93 to Leu96, is ambiguous at this stage, (b) In each of...

Complete results are shown in Table II. Column 2 lists the speed Columns 3 and 4 show the results of the fitting technique described above. Columns 5 and 6 indicate the interfacial compositions, Column 7 lists the root-mean square difference between calculated and experimentally measured heights, and the final column lists the e values for each run. 

Figure 7 Bottom water simulated by the model (color-shaded field) and from data (colored dots). The mean model-data difference in areas not affected by bomb- C is only + 1.3%o, and the root-mean-square difference amounts to only 5.2%o. From Schlitzer R (2006) Assimilation of radiocarbon and chlorofluorocarbon data to constrain deep and bottom water transports in the world ocean. Journal of Physical Oceanography 37 259-276.

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