Structure superposition tools: Difference between revisions
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 11: | Line 11: | ||
==Recommendation== | ==Recommendation== | ||
'''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 [[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. | ||
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]]). | 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]]). | ||