Content deleted Content added
m remove URL redundant with identifier in autolinked citation |
rm item linked in text; typo |
||
Line 20:
Algorithms based on multidimensional rotations and modified [[quaternion]]s have been developed to identify topological relationships between protein structures without the need for a predetermined alignment. Such algorithms have successfully identified canonical folds such as the [[helix bundle|four-helix bundle]].<ref name="Diederichs"/> The [http://wishart.biology.ualberta.ca/SuperPose/ SuperPose] method is sufficiently extensible to correct for relative ___domain rotations and other structural pitfalls.<ref name="Maiti"/>
===Evaluating
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 correlation 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"/>
Line 179:
{{col div|colwidth=30em}}
* [[Multiple sequence alignment]]
* [[List of sequence alignment software
* [[Structural Classification of Proteins]]
* [[SuperPose]]
| |||