Structure superposition tools: Difference between revisions
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''Structural alignment'' refers to the alignment, in three dimensions, between two or more molecular models. In the case of proteins, this is usually performed without reference to the sequences of the proteins. This may suggest evolutionary relationships that are not discernable from sequence comparisions. | ''Structural alignment'' refers to the alignment, in three dimensions, between two or more molecular models. In the case of proteins, this is usually performed without reference to the sequences of the proteins. This may suggest evolutionary relationships that are not discernable from sequence comparisions. | ||
The purpose of this article is to help in choosing a server or software package for performing structural alignment. Characteristics of structural alignment servers and software packages are listed, along with results of testing with a few examples. | |||
==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). | 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 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. | ||