[ssml] Re: precomputed SCOP domain superpositions?

[Mensur Dlakic]

Hi Dan,

If you are interested only in pairs of structures, then CE is what you 
need. Server (including binaries) can be found at:

http://cl.sdsc.edu/ce.html

Many (most?) structural alignments are already pre-computed. If you want to 
do your own alignments of many structures, I suggest installing a binary 
because the server is just too cumbersome to use.

The output for comparing two structures is below. It contains the alignment 
and some statistics, including RMSD. Structures with Z-scores higher than 
4-4.5 are definitely related regardless of RMSD, though I have seen some 
scores between related structures that were lower than 4. Finally, the 
X2,Y2,Z2 transformations at the very bottom tell you what you need to do to 
coordinates of chain 2 (1SMT in this case) to superimpose it to chain 1. I 
wrote a small program that will take these numbers and the original PDB 
file to produce superimposed structure - I could probably make binaries for 
Windows, Linux and possibly Sparc-solaris 2.9.

Hope this helps,

Mensur


Structure Alignment Calculator, version 1.02, last modified: Jun 15, 2001.

CE Algorithm, version 1.00, 1998.

Chain 1: 1JGS.pdb:A (Size=138)
Chain 2: 1SMT.pdb:A (Size=122)

Alignment length = 80 Rmsd = 1.85A Z-Score = 5.2 Gaps = 7(8.8%) CPU = 2s 
Sequence identities = 13.6%

Chain 1:   30 
LDI-TAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGG
Chain 2:   41 
AVLADPNRLRLLSLLARS-ELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ---GRHVYYQLQD--

Chain 1:   99 AAICEQCHQLVGQDLHQE
Chain 2:  105 HHIVALYQNALDHLQECR

      X2 = ( 0.091878)*X1 + (-0.159286)*Y1 + ( 0.982948)*Z1 + (  -10.019566)
      Y2 = (-0.992630)*X1 + (-0.092983)*Y1 + ( 0.077715)*Z1 + (   31.907251)
      Z2 = ( 0.079018)*X1 + (-0.982844)*Y1 + (-0.166655)*Z1 + (   80.906204)


At 08:51 AM 8/26/2004, you wrote:

>I would like to just get the 'structural similarity' score between scop
>domains. i.e. RMSD between a pair. Is this possible with cemc?
>
>Ta,
>Dan.

==========================================================================
| Mensur Dlakic, PhD                | Tel: (406) 994-6576                |
| Department of Microbiology        | Fax: (406) 994-4926                |
| Montana State University          |                                    |
| 109 Lewis Hall, P.O. Box 173520   | http://myprofile.cos.com/mensur    |
| Bozeman, MT 59717-3520            | E-mail: mdlakic at montana.edu        |
==========================================================================