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Typically RMSD is used as a quantitative measure of similarity between two or more protein structures. For example, the CASP protein structure prediction competition uses RMSD as one of its assessments of how well a submitted structure matches the known, target structure. Thus the lower RMSD, the better the model is in comparison to the target ...
In experimental psychology, the RMSD is used to assess how well mathematical or computational models of behavior explain the empirically observed behavior. In GIS, the RMSD is one measure used to assess the accuracy of spatial analysis and remote sensing. In hydrogeology, RMSD and NRMSD are used to evaluate the calibration of a groundwater ...
In the physics of gas molecules, the root-mean-square speed is defined as the square root of the average squared-speed. The RMS speed of an ideal gas is calculated using the following equation: v RMS = 3 R T M {\displaystyle v_{\text{RMS}}={\sqrt {3RT \over M}}}
Let P and Q be two sets, each containing N points in .We want to find the transformation from Q to P.For simplicity, we will consider the three-dimensional case (=).The sets P and Q can each be represented by N × 3 matrices with the first row containing the coordinates of the first point, the second row containing the coordinates of the second point, and so on, as shown in this matrix:
A molecular dynamics simulation requires the definition of a potential function, or a description of the terms by which the particles in the simulation will interact. In chemistry and biology this is usually referred to as a force field and in materials physics as an interatomic potential.
In probability theory and statistics, the coefficient of variation (CV), also known as normalized root-mean-square deviation (NRMSD), percent RMS, and relative standard deviation (RSD), is a standardized measure of dispersion of a probability distribution or frequency distribution.
where = is the reduced Planck constant.. The quintessentially quantum mechanical uncertainty principle comes in many forms other than position–momentum. The energy–time relationship is widely used to relate quantum state lifetime to measured energy widths but its formal derivation is fraught with confusing issues about the nature of time.
Examples of correlation between RCI and other methods of measuring motional amplitudes in proteins. NMR RMSD - root mean square fluctuations of atomic coordinates in NMR ensembles, MD RMSD - root mean square fluctuations of atomic coordinates in MD ensembles, S2 - model-free order parameter, RCI - random coil index, B-factor - temperature factor of X-ray structures; RCI->NMR RMSD - root mean ...