Structure superposition tools: Difference between revisions
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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. | 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. | ||
== | Wikipedia offers a [http://en.wikipedia.org/wiki/Structural_alignment_software list of structural alignment software packages] and an overview of [http://en.wikipedia.org/wiki/Structural_alignment structural alignment]. Hasegawa and Holm reviewed structural alignment methods in 2009<ref>PMID: 19481444</ref>. | ||
==Evaluating Structural Alignments== | |||
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 Å 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 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 Å 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 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. | ||
I found NO way to color the alignment by RMSD in Jmol. Both [[#DeepView = Swiss-PDBViewer]] and [[#PyMOL]] color alignments by RMSD but the results cannot be exported to Jmol. | I found NO way to color the alignment by RMSD in Jmol. Both [[#DeepView = Swiss-PDBViewer]] and [[#PyMOL]] color alignments by RMSD but the results cannot be exported to Jmol. | ||
==Recommendation== | ==Recommendation== | ||
There are several well-documented, easy to use servers that do an excellent job of sequence-independent structural alignment, described below. These servers generally out-perform the stand-alone applications [[#DeepView = Swiss-PDBViewer]] and [[#PyMOL]]. | |||
'''Opinion''' ([[User:Eric Martz|Eric Martz]] 03:18, 5 October 2010 (IST)): FATCAT appears, in my limited testing, to equal or out-perform the other servers listed below, both for rigid and flexible structural alignment, as well as being one of the easiest to use. See [[#FATCAT example]] and [[#Example Requiring Flexibility]]. The best-documented use is at its server, [http://fatcat.burnham.org fatcat.burnham.org]. It can also be used at [http://www.pdb.org pdb.org] either directly in their website, or via their java web start application (see instructions below under [[#Calculate Structure Alignment]]). The fact that FATCAT offers both rigid and flexible structural alignments is a further advantage. Also, it produces a [[morphs|morph]] which helps greatly in visualizing the relationship between two aligned models. | '''Opinion''' ([[User:Eric Martz|Eric Martz]] 03:18, 5 October 2010 (IST)): FATCAT appears, in my limited testing, to equal or out-perform the other servers listed below, both for rigid and flexible structural alignment, as well as being one of the easiest to use. See [[#FATCAT example]] and [[#Example Requiring Flexibility]]. The best-documented use is at its server, [http://fatcat.burnham.org fatcat.burnham.org]. It can also be used at [http://www.pdb.org pdb.org] either directly in their website, or via their java web start application (see instructions below under [[#Calculate Structure Alignment]]). The fact that FATCAT offers both rigid and flexible structural alignments is a further advantage. Also, it produces a [[morphs|morph]] which helps greatly in visualizing the relationship between two aligned models. | ||