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===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" /> Many methods output some sort of "score" indicating the quality of the superposition. 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 correlation to the true E-value. That is,
Different methods will superimpose different numbers of residues because they use different quality assurances and different definition 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" />
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