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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 ...
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) ).
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).
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).
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.
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