Root mean square difference RMSD

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. 

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...

There are very few differences between the structures of l-Ppol we solved with and without magnesium bound. In fact after superposition, the polyalanine root mean square difference (rmsd) (0.13 A) is less than the rmsd between the two monomers in the asymmetric unit (see below). Even the water sites in the region of the metal binding site are similar. Magnesium binding only shifts the location of solvent water sites slightly. Since the two structures are so similar, we will focus on the l-Ppol structure without DNA in the presence of Mg2+. 

The SEP is calculated as the root mean square differences (RMSD), also known as a mean square for residuals for IV - 1 degrees of freedom. It allows for comparison between NIR-observed predicted values and wet laboratory values. The SEP is generally greater than the SEC but could be smaller in some cases due to chance alone. When calculating the SEP, it is critical that the constituent distribution be uniform and the wet chemistry be very accurate for the validation sample set. If these criteria are not met for validation sample sets, the calculated SEP may not have validity as an accurate indicator of overall calibration performance. To summarize, the SEP is the square root of the mean square for residuals for - 1 degrees of freedom, where the residual equals actual minus predicted for samples outside the calibration set. 

The differences between ab initio and molecular mechanics generated dipole moments were discussed. The MM3(2000) force field is better able to reproduce experimental dipole moments for a set of forty-four molecules with a root mean squared deviation (rmsd) of 0.145 Debye compared with Hartree-Fock (rmsd 0.236 Debye), M0ller-Plesset 2 (rmsd 0.263 Debye) or MM3(96) force field (rmsd 0.164 Debye). The orientation of the dipole moment shows that all methods give comparable angle measurements with only small differences for the most part. This consistency within methods is important information and encouraging since the direction of the dipole moment cannot be measured experimentally. 

Moreover, the objective function obtained by minimizing the square of the difference between the mole fractions calculated by UNIQUAC model and the experimental data. Furthermore, he UNIQUAC structural parameters r and q were carried out from group contribution data that has been previously reported [14-15], The values of r and q used in the UNIQUAC equation are presented in table 4. The goodness of fit, between the observed and calculated mole fractions, was calculated in terms RMSD [1], The RMSD values were calculated according to the equation of percentage root mean square deviations (RMSD%) ... 

Table 8.2 Root mean square deviation (RMSD) of the backbone of the aligned models of the h AR. The main difference among the models is due to the loops, which represent the most variable region of the templates and consequently of the models. Particular attention has to be given to EL2 because it is part of the binding pocket and it can directly interact with ligands...

When the square variable is a difference between values predicted by a model or an estimator and the values actually observed, this quantity take the name of root mean square deviation RMSD or root mean square error, RMSE) and is among the regression parameters. 

Fig. 29 Detailed root-mean-square displacement (RMSD) A, per residue, of the geometric difference between the apo hPNP-hPNP guanine (black), and apo hPNP-hPNP ImmH (red) crystal structure pairs. The different RMSDs of both pairs of crystals, provide evidence that the TS analog is bound to hPNP much tighter than the substrate analog.

We have recently used MD simulations to explore the differences in the structure, energetics, and dynamics of protein hydration water in N and MG states of HaLA. The MG state was modeled as an ensanble of 15 conformers prepared as summarized above in Section 16.2 and described in detail in Ref [5]. The root-mean squared deviation (RMSD) of the backbone heavy atom positions from the initial crystal structure ranged from 2.8 to 7.6 A, which is significantly greater than the 1.1 A RMSD of the N state simnlation. Radii of gyration demonstrated the loss of compaction of the MG conformers (R = 15.2-17.8 A) compared to the N state (R. = 14.3 A). The increase in size is accompanied by a modest increase in the... 

Several techniques are available for similarity measures on three-dimensional stmctures. The most common technique is structure superposition or superimposition. In this technique, one stmcture is rotated or reoriented until it ean be superimposed onto the other stmcture (Wishart, 2005). The proeedure starts with identifying common reference points. As soon as these points are identified, one of the stmctures is rotated until these common reference points are almost matching with minimum differences, that is, minimal distance between equivalent positions on the protein stmcture. One of the most commonly used distance measures is root mean-square deviation (RMSD) (Xiong, 2006), determined as... 

RMSD root mean square difference RTW room temperature wet... 

FIGURE 4.1 Example of different conformation accuracy levels, as measured by root mean squared deviation (RMSD). This example shows computationally generated conformations of axitinib (light gray) at various levels of dissimilarity to one particular crystallographic structure (dark gray). 

The root-mean-square deviation (rmsd) can be taken to be a measure of the precision of the correlations. The rmsd value was calculated from the difference between the experimental and calculated mole fractions according to the following equation. 

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