Structure superposition tools: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

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

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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. Hasegawa and Holm reviewed structural alignment methods in 2009<ref>PMID: 19481444</ref>.
+''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 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 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.
+==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 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.
 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].
-==Overview==
+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]]. Hasegawa and Holm reviewed structural alignment methods in 2009<ref>PMID: 19481444</ref>.
-There are several well-documented, easy to use servers that do an excellent job of sequence-independent structural alignment. These servers generally out-perform the stand-alone applications [[#DeepView = Swiss-PDBViewer]] and [[#PyMOL]].
 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.