[BiO BB] Getting PDB id from Swissprot entry

D. Norris dmnunif at charter.net
Thu Jul 1 22:51:01 EDT 2004


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 !!!

----- 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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