Editing Structural alignment (section)

===Evaluating similarity===
Often the purpose of seeking a structural superposition is not so much the superposition itself, but an evaluation of the similarity of two structures or a confidence in a remote alignment.<ref name="casp11"/><ref name="Malmstrom" /><ref name="robetta"/> A subtle but important distinction from maximal structural superposition is the conversion of an alignment to a meaningful similarity score.<ref name="Mammoth" /><ref name="ZhangTMscore"/> Most methods output some sort of "score" indicating the quality of the superposition.<ref name="zemla" /><ref name="fischer"/><ref name="poleksic"/><ref name="Mammoth"/><ref name="ZhangTMscore"/> However, what one actually wants is ''not'' merely an ''estimated''  "Z-score" or an ''estimated'' E-value of seeing the observed superposition by chance but instead one desires that the ''estimated'' E-value is tightly correlated to the true E-value. Critically, even if a method's estimated E-value is precisely correct ''on average'', if it lacks a low standard deviation on its estimated value generation process, then the rank ordering of the relative similarities of a query protein to a comparison set will rarely agree with the "true" ordering.<ref name="Mammoth"/><ref name="ZhangTMscore"/>

Different methods will superimpose different numbers of residues because they use different quality assurances and different definitions of "overlap"; some only include residues meeting multiple local and global superposition criteria and others are more greedy, flexible, and promiscuous.  A greater number of atoms superposed can mean more similarity but it may not always produce the best E-value quantifying the unlikeliness of the superposition and thus not as useful for assessing similarity, especially in remote homologs.<ref name="casp11"/><ref name="Malmstrom" /><ref name="robetta" /><ref name="skolnick" />