Rmsd values, between structures

Fig. 2.1. The backbone structures of authentic and recombinant goat a-lactalbumin in the crystal form. The backbone of Mol A of the authentic protein, represented by a wire model, was superimposed on the backbone of the recombinant protein. Gray and black wires represent the authentic and recombinant proteins, respectively. The C -atom RMSD value between the two proteins was 0.54 A. The PDB codes for the authentic and recombinant proteins are 1HFY and 1HMK, respectively...

An useful step made in this study was to compare 15 energy minimised structures, selected initially from the dynamics trajectory at 10 ps intervals. Pairwise RMSD values between these structures varied between 1.3 A and 1.9 A. (over the backbone atoms of headpiece and the operator, excluding the terminal base-pairs). All the structures were rather similar and acceptable from both stereochemical and NMR points of view. It was nevertheless found that several different protein-DNA hydrogen bonding arrangements were possible and could not be discriminated on the basis of the conformational energy. 

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%) ... 

Fig. 2.13. The probability distributions of four structural parameters calculated for the structures of each cluster [25]. (a) The fraction of the native tertiary contacts Q. (b) The RMSD value of Ca atoms between a pair of structures that belong to the same cluster. The SASA for (c) hydrophobic and (d) hydrophilic side chains. Reproduced with permission from [25]...

The rmsd value is elucidated in two different manners. A pair-wise-averaged rmsd is calculated by averaging for rmsd values among atomic positions in every pair of coordinates. A residue-averaged rmsd is calculated by rms deviations for all of the superimposed structures followed by averaging for residues. The residue-averaged rmsd is considerably smaller than the pair-wise-averaged rmsd therefore, the manner should be notified. A pair-wise rmsd value is a distance between two conformers in the conformational space thereby, it can be used as a measure for the conformational search extent (Section 7.2). 

Information on the second hydration shell of ions is much poorer than that of the first hydration shell (see Table 3). The quantitative analysis of radical distribution curves in the long r range is difficult and much less reliable. Reliable information in the structure of the second shell may be obtained by the isomorphous substitution method in XRD measurements and the isotopic substitution method in ND measurements. Of course, such methods cannot be applied to every electrolyte solution. In most works in which some attempts have been made to determine the structure of the second hydration shell of ions, suitable structural models have been introduced. In some other cases fitting procedures between experimental and theoretical G r) functions have been continued until a more or less satisfactory agreement is obtained between them. Details about the distance between a central ion and water molecules in the second hydration shell, mo(2), the rmsd, /mo(2), the number of water molecules in the second hydration shell of the ion, mo(2), and /o(i) o(2) and /o(i) o(2) values between water molecules in the first and second hydration shells are given in Ohtaki and Radnai (1993). ... 

As in the trp repressor-consensus ODNA complex, residues 4 to 19 (monomer I) and residues 504 and 519 (monomer II) appear as a coil in our structure due to the lack of NOE constraints. All backbone atom positions in the core (helices A, B, C and F) are well defined in both monomers. The backbone atom positions in helix D are not as well defined as those in the rest of the sequence. Both the backbone and side chain atoms at the N-terminal part of helix C and the turn between helices C and D have larger than average RMSD values, as a consequence of the reduced number of constraints in these regions. 

The normalized RMSD(i, j)ioo values between all the conformations in each trajectory are represented by a colour in Fig. 5. The colour scale, seen on the top right, is in A and is the same for all 8 trajectories. The more to the blue a value is, the more similar the two structures being compared are and the least fiexible the protein is, and the more red a value is, the greater the... 

Fig. 3. Flexible protocol results for AR structures 3B68 and 3L3X re-docked (A and D) and cross-docked (B and C) with B68 and DHT. Here we show the docked poses with the highest energy of binding (blue column) predicted using the rigid backbone taken from the X-ray structure and the snapshots from MD, SMD and low-frequency vibrations. In addition we report the results obtained using the tool mod-VINA. To establish the accuracy of the prediction we reported the RMSD values (green column) calculated between the docked pose and the experimental one (Color figure online).

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