Structure superposition tools: Difference between revisions

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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,128 edits
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[[#FATCAT]] offers a [[morphs|morph]] in Jmol that helps to visualize the structural relationship between the two aligned models.
[[#FATCAT]] offers a [[morphs|morph]] in Jmol that helps to visualize the structural relationship between the two aligned models.


==Recommendation==
==Conclusions==
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]].  
There are several well-documented, easy to use servers that do an excellent job of sequence-independent structural alignment, described below. These servers appear to out-perform the stand-alone applications [[#DeepView = Swiss-PDBViewer]] and [[#PyMOL]]. They include
* [[#CE|CE]] rigid alignment only (see below).
* [[#Dali|Dali]] rigid alignment only. Colors by ''structure conservation'' distinguishing aligned from non-aligned segments.
* [[#FATCAT|FATCAT]] '''flexible''' and rigid alignment. Generates morph of alignment.
Although the CE server appears not to be well maintained, the CE and FATCAT algorithms can 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]]).


'''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.
If you want automated selection of a small subdomain with the best possible alignment, 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]]).
 
If you want automated selection of a subdomain with the best possible alignment, try [[#DeepView = Swiss-PDBViewer]]'s ''Explore Domain Alternate Fits'' or ''Iterative Magic Fit'' (see results in the [[#DeepView = Swiss-PDBViewer example]]).


==Structural Alignment Servers==
==Structural Alignment Servers==
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