Structure superposition tools: Difference between revisions
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==Overview== | ==Overview== | ||
The structural differences between two optimally aligned models are usually measured as the Root Mean Square Distance ('''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>PMID: 3709526</ref>. <ref "3dcrunch">PMID: 10865955</ref>. | The structural differences between two optimally aligned models are usually measured as the Root Mean Square Distance ('''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 Å RMSD<ref name="chothia86" /><ref "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 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. | ||
