Structure superposition tools: Difference between revisions

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Eric Martz, Markus Wiederstein, Wayne Decatur, Ronald Ayoub, Joel L. Sussman, Angel Herraez

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 Wikipedia offers a [http://en.wikipedia.org/wiki/Structural_alignment_software list of structural superposition software packages] and an overview of [http://en.wikipedia.org/wiki/Structural_alignment structural superposition]. Hasegawa and Holm reviewed structural superposition methods in 2009<ref>PMID: 19481444</ref>.
-==Evaluating Structural Alignments==
+==Evaluating Structural Superpositions==
-The structural differences between two optimally aligned models are usually measured as the [http://en.wikipedia.org/wiki/RMSD Root Mean Square Deviation] ('''RMSD''') between the aligned alpha-carbon positions (excluding deviations from the non-aligned positions). To provide a frame of reference for RMSD values, note that up to 0.5 Å RMSD of alpha carbons occurs in independent determinations of the same protein<ref name="chothia86">PMID: 3709526</ref>. Crystallographic models of proteins with about 50% sequence identity differ by about 1 &Aring; RMSD<ref name="chothia86" /><ref name="3dcrunch">PMID: 10865955</ref>. Deviations can be much larger for models determined by [[NMR]]<ref name="3dcrunch" />.
+The structural differences between two optimally superposed models are usually measured as the [http://en.wikipedia.org/wiki/RMSD Root Mean Square Deviation] ('''RMSD''') between the superposed alpha-carbon positions (excluding deviations from the non-superposed positions). To provide a frame of reference for RMSD values, note that up to 0.5 Å RMSD of alpha carbons occurs in independent determinations of the same protein<ref name="chothia86">PMID: 3709526</ref>. Crystallographic models of proteins with about 50% sequence identity differ by about 1 &Aring; RMSD<ref name="chothia86" /><ref name="3dcrunch">PMID: 10865955</ref>. Deviations can be much larger for models determined by [[NMR]]<ref name="3dcrunch" />.
-The statistical significance of a structural alignment, relative to an alignment of random sequence-nonredundant structures in the [[PDB]], is usually measured with a '''[http://en.wikipedia.org/wiki/Standard_score z-score]'''. The z-score is the distance, in standard deviations, between the observed alignment RMSD and the mean RMSD for random pairs of the same length, with the same or fewer gaps. Z-scores less than 2 are considered to lack statistical significance.
+The statistical significance of a structural superposition, relative to a superposition of random sequence-nonredundant structures in the [[PDB]], is usually measured with a '''[http://en.wikipedia.org/wiki/Standard_score z-score]'''. The z-score is the distance, in standard deviations, between the observed alignment RMSD and the mean RMSD for random pairs of the same length, with the same or fewer gaps. Z-scores less than 2 are considered to lack statistical significance.
+When the models being compared have substantial differences, and especially if they have multiple domains, different estimates of the closenss of fit have been employed, notably in [[CASP]].
 ==Visualizing Structural Alignments==