[ssml] Re: precomputed SCOP domain superpositions?

Mensur Dlakic mdlakic at montana.edu
Tue Aug 24 11:41:31 EDT 2004


This site may help:


It says:

DMAPS stores pre-calculated multiple protein structure alignments for all 
chains in PDB. There are 28508 chains in PDB clustered into 2618 families. 
Multiple structure alignments were calculated based on 
<http://cl.sdsc.edu/mc/mc.html>CE-MC algorithm and the output was formatted 
using <http://www-cryst.bioc.cam.ac.uk/~joy/>JOY program. Users will be 
able to retrieve multiple alignments of corresponding family, for any given 
PDB chain. For some families, JOY formatting was not successful in which 
case, users should be able to view the alignments in TEXT format.

They are not sorted according to SCOP, but that part you can do on your 
own. I have done multiple structural alignments of most of SCOP families, 
but that is yet to be published...



At 06:23 AM 8/24/2004, you wrote:
>Are there precomputed all-against-all pairwise structure superpositions
>of SCOP domains available somewhere? The superpositions may be
>computed by programs like CE, DALI, VAST, ...
>We would prefer recent SCOP versions.
>Thanks a lot for your help,
>   Mario

| Mensur Dlakic, PhD                | Tel: (406) 994-6576                |
| Department of Microbiology        | Fax: (406) 994-4926                |
| Montana State University          |                                    |
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