[BiO BB] Getting PDB id from Swissprot entry

[D. Norris]

Dr. Chandra:

If Sourangshu's question is really relevant to bioinformatics in a whole
biological system, then dmn thinks there must be some relevance to our
thread..

dmn
----- Original Message ----- 
From: "Dr.Nagasuma Chandra" <nchandra at physics.iisc.ernet.in>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Friday, July 02, 2004 4:07 AM
Subject: Re: [BiO BB] Getting PDB id from Swissprot entry


>
> I agree too and would ask the same question that Dan asked, but dont see
> the relevance of this thread to the specific question Sourangshu asked.
>
> Sourangshu, if you are looking for the exact match, then fetching the DR
> lines is the simplest, but what Iddo said still holds good (of many-many
> matches in some cases, part domain/missing loops in some cases)- all
> depends on what you are looking for.
>
> Nagasuma Chandra
>
> ***********************************************
>    Dr. Nagasuma Chandra
>    Bioinformatics centre
>    Indian Institute of Science
>    Bangalore 560 012
>    Tel: +91-80-22932469 or 23601409
>    Fax: +91-80-23600551
>    e-mail: nchandra at physics.iisc.ernet.in
> ***********************************************
>
>
> On Fri, 2 Jul
> 2004, Dan Bolser wrote:
>
> > On Thu, 1 Jul 2004, D. Norris wrote:
> >
> > >Hi:
> > >
> > >Meaningful bioinformatics must work in the whole cell, and whole
> > >multicellular organism. Genomics and proteomics alone are just lists of
> > >parts--no more, no less !!!
> >
> > I agree, but can you suggest a 'whole cell' or 'organism' framework that
I
> > can use?
> >
> > dan
> >
> > >
> > >dmn
> > >----- Original Message ----- 
> > >From: "Dan Bolser" <dmb at mrc-dunn.cam.ac.uk>
> > >To: <bio_bulletin_board at bioinformatics.org>
> > >Cc: <ssml at bioinformatics.org>
> > >Sent: Wednesday, June 30, 2004 8:32 AM
> > >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry
> > >
> > >
> > >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote:
> > >>
> > >> >Hi,
> > >> >
> > >> >Is there a direct way (without reading the protein name from
swissprot
> > >> >and searching in PDB) of getting the PDB id of the protein
corresponding
> > >> >to a particular Swissprot id ?
> > >>
> > >> I would use the MSD database, which maintains a manually curated
version
> > >> of the SwissProt to PDB mapping.
> > >>
> > >> >Also, how do I know whether structure for a particular protein
> > >> >corresponding to a swissprot id has been determined or not ?
> > >>
> > >> Strictly speeking, the above mapping gives you this. More
realistically,
> > >> however, you can consider very close homologues to the above set as
also
> > >> 'solved'. Where you draw the line is a matter of requirement, but you
can
> > >> get reasonable models (allegedly) at > 40% sequence identity, or
> > >> reasonable 'fold prediction' at much larger distances (see
SUPERFAMILY for
> > >> example).
> > >>
> > >> It all depends on what you want to do.
> > >>
> > >> >Thank you very much..
> > >> >
> > >> >Regards,
> > >> >Sourangshu.
> > >> >
> > >> >
> > >>
> > >> _______________________________________________
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> > >
> > >
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>
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