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In many cases, especially for smaller samples, the sample range is likely to be affected by the size of sample which would hamper comparisons. Another possible method to make the RMSD a more useful comparison measure is to divide the RMSD by the interquartile range (IQR).
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 ...
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 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) ).
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).
Naz Reid had 27 points, 13 rebounds and seven assists for the short-handed Minnesota Timberwolves in a 116-101 victory over Oklahoma City on Thursday night that stopped the Thunder's seven-game ...
Essentially the CV(RMSD) replaces the standard deviation term with the Root Mean Square Deviation (RMSD). While many natural processes indeed show a correlation between the average value and the amount of variation around it, accurate sensor devices need to be designed in such a way that the coefficient of variation is close to zero, i.e ...
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 ...