Structure superposition tools: Difference between revisions
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==Conclusions== | ==Conclusions== | ||
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 | 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|DeepView = Swiss-PDBViewer]] and [[#PyMOL|PyMOL]]. They include | ||
* [[#CE|CE]] rigid alignment only (see below). | * [[#CE|CE]] rigid alignment only (see below). | ||
* [[#Dali|Dali]] rigid alignment only. Colors by ''structure conservation'' distinguishing aligned from non-aligned segments. | * [[#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. | * [[#FATCAT|FATCAT]] '''flexible''' and rigid alignment. Generates morph of alignment. | ||
Although the CE server appears not to be well maintained, the CE | Although the CE server appears not to be well maintained, the CE 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|Calculate Structure Alignment]]). | ||
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 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]]). | ||
