Structure superposition tools: Difference between revisions
Eric Martz (talk | contribs) |
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===CE=== | ===CE=== | ||
The ''Combinatorial Extension'' | The ''Combinatorial Extension'' method. See the [http://en.wikipedia.org/wiki/Structural_alignment#Combinatorial_extension explanation of CE methodology at Wikipedia]. | ||
*Server: [http://cl.sdsc.edu/ CE Home Page]. | *Server: Use [http://rcsb.org rcsb.org] At the main page, click on Analyze, then on Pairwise Structure Alignment.<!--[http://cl.sdsc.edu/ CE Home Page].--> | ||
*Publication (1998)<ref>PMID: 9796821</ref> | *Publication (1998)<ref>PMID: 9796821</ref> | ||
*'''N.B. Database of structure neighbors has not been updated since 2004. Java applet for viewing results is not working in Sept. 2010. Finding structure neighbors from the entire PDB database ("ALL") appears to have been broken since 2001.''' | <!--*'''N.B. Database of structure neighbors has not been updated since 2004. Java applet for viewing results is not working in Sept. 2010. Finding structure neighbors from the entire PDB database ("ALL") appears to have been broken since 2001.'''--> | ||
*Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />) | *Rigid alignment: ONLY (according to FATCAT<ref name="fatcat" />) | ||
*Align DNA? NO. | *Align DNA? NO. | ||
*Align multiple protein chains? NO. Aligns one pair of chains at a time. | *Align multiple protein chains? NO. Aligns one pair of chains at a time. | ||
*Structure-based sequence alignment: YES. | *Structure-based sequence alignment: YES. | ||
*Visualization: | *Visualization: Mol*. | ||
*Offered by RCSB? YES. | *Offered by RCSB? YES. | ||