[BiO BB] Getting PDB id from Swissprot entry

Dr.Nagasuma Chandra nchandra at physics.iisc.ernet.in
Fri Jul 2 05:07:40 EDT 2004


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.
> >> >
> >> >
> >>
> >> _______________________________________________
> >> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
> >
> >_______________________________________________
> >BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
> 
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 





More information about the BBB mailing list