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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 ...
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 ...
The sample Taylor diagram shown in Figure 1 [16] provides a summary of the relative skill with which several global climate models simulate the spatial pattern of annual mean precipitation. Eight models, each represented by a different letter on the diagram, are compared, and the distance between each model and the point labeled “observed ...
The maximum is taken over all possible structure superpositions of the model and template (or some sample thereof). When comparing two protein structures that have the same residue order, L common {\displaystyle L_{\text{common}}} reads from the C-alpha order number of the structure files (i.e., Column 23-26 in Protein Data Bank (file format) ).
A free PyMol plugin easily implementing Kabsch is . (This previously linked to CEalign , but this uses the Combinatorial Extension (CE) algorithm.) VMD uses the Kabsch algorithm for its alignment. The FoldX modeling toolsuite incorporates the Kabsch algorithm to measure RMSD between Wild Type and Mutated protein structures.
The MSE either assesses the quality of a predictor (i.e., a function mapping arbitrary inputs to a sample of values of some random variable), or of an estimator (i.e., a mathematical function mapping a sample of data to an estimate of a parameter of the population from which the data is sampled).
The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.
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 ...