[Fwd: [Fwd: Proteins comparison]]

[Ivan Torshin]

Hello, following are the answers to the question for pdb-l list.
best regards,
Ivan.

Subject: 
         Re: [Fwd: Proteins comparison]
   Date: 
         Fri, 2 Jul 1999 09:34:26 +0100 (GMT Daylight Time)
   From: 
         Geoff Barton <geoff at ebi.ac.uk>
     To: 
         Ivan Torshin <TIY at phys.chem.msu.ru>
     CC: 
         PDB-L list <pdb-l at rcsb.org>




There are a number of different techniques around for comparing protein
three dimensional structures.  Some are available as WWW servers. This is
certainly NOT a complete list so apologies to anyone I've left out, but
you might try DALI at EBI (http://www2.ebi.ac.uk/dali), CATH at UCL
(http://www.biochem.ucl.ac.uk/bsm/cath/server/index.html) and VAST at NCBI
(http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html).  Each has
its own way of scoring similarity.

Many programs are also downloadable so that you can run them on your own
computer. One available from me is STAMP which is a suite of programs
for pairwise and multiple structure alignment, database searching and
general manipulation of protein coordinate files (see
http://barton.ebi.ac.uk/ and click on 'software').

Hope this helps,

Geoff.


On Thu, 1 Jul 1999, oded wrote:

> Ivan Torshin wrote:
> 
> > Subject: Proteins comparison
> > Date: Thu, 1 Jul 1999 17:04:42 +0200
> > From: "Philippe CHAVATTE" <pchavatt at phare.univ-lille2.fr>
> > Organization: Universite des Sciences et Technologies de LILLE, France
> > To: molmodel at hgmp.mrc.ac.uk
> >
> > What is the best methodology to compare two protein 3D structures (pdb
> > format) ?
> > What criteria permit to affirm their similarity ?
> > Many thanks for your help.
> >
> > Philippe
> >
> > -----------------
> >
> > Philippe CHAVATTE
> > Institut de Chimie Pharmaceutique Albert Lespagnol
> > BP 83
> > 59006 LILLE CEDEX
> > FRANCE
> >
> > E-Mail : pchavatt at phare.univ-lille2.fr
> 
> --
> ----------------------------------------------------------------
>  " If we knew what it was we were doing,
>    it would not be called research,
>    would it?"
>                      Albert Einstein (1879-1955)
> ----------------------------------------------------------------
> Oded Livneh                                   E-mail:
> oded at compugen.co.il
> Compugen Ltd.                              Tel:            +972-3-765-8585
> 
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> Tel-Aviv 69512, Israel                   Fax:           +972-3-765-8555
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> 
> 
> 
> 
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------------------
Dr Geoff. Barton, EMBL-European Bioinformatics Institute, Genome Campus, 
Hinxton, Cambs CB10 1SD, U.K., mailto:geoff at ebi.ac.uk
http://barton.ebi.ac.uk, Tel: +44 1223 494414, Fax: +44 1223 494496
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