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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 ===Protein structural superposition===
 There are several well-documented, easy to use servers and software packages that do an excellent job of sequence-independent structural superposition, described below.  They include
-* [[#CE|CE]] rigid superposition only (see Note below).
+* [[#CE|CE]] rigid superposition only (see Note* below).
 * [[#Dali|Dali]] rigid superposition only. Jmol. Colors by ''structure conservation'' distinguishing closely superposed from poorly superposed segments.
 * [[#FATCAT|FATCAT]] '''flexible''' and rigid superposition. Jmol. Generates '''morph''' of alignment.
 * [[#TopMatch|TopMatch]]
-Note: Although the CE server appears not to be well maintained, the CE algorithms can be used at [http://www.rcsb.org rcsb.org] either directly in their website, or via their java web start application (see instructions below under [[#Calculate Structure Alignment|Calculate Structure Alignment]]). Both of the latter methods include visualization in Jmol (not available at the CE website).
+*Note: Although the CE server appears not to be well maintained, the CE algorithms can be used at [http://www.rcsb.org rcsb.org] (see instructions below under [[#Calculate Structure Superposition|Calculate Structure Superposition]]).
 If you want automated selection of a small subdomain with the best possible superposition, try [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]]'s ''Explore Domain Alternate Fits'' or ''Iterative Magic Fit'' (see results in the [[#DeepView = Swiss-PDBViewer example|DeepView = Swiss-PDBViewer example]]).