[BiO BB] Getting PDB id from Swissprot entry

[Dan Bolser]

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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