[BiO BB] Getting PDB id from Swissprot entry

[Dan Bolser]

On Sat, 3 Jul 2004, D. Norris wrote:

>Hi Dan:
>
>We at Unifinium Ltd., and the University of Wisconsin-Madison, have worked,
>quite effectively we think, on bioinformatics for about 40 years using whole
>live insect systems, and about 11 standardized in vitro systems extracted
>from the whole insect biological system. Data obtained from any of the in
>vitro systems can be readily translated into the data (i.e., biological
>information) obtained by any of the other in vitro systems, and into the
>ultimate behavioral change induced in the whole insect system by the abiotic
>(affector) messenger (e.g., feeding inhibitor, or kairomone). Our continuing
>major (central)experimental focus has been on the involved qualitative and
>quantitative changes in the electrochemistry of proteins. We have had much
>fun, and believe that we have made very meaningful contributions to
>bioinformatics. Redox (exchange) chemistry is very central in our findings.
>Pretinent publications involving Norris, and associates, start in ~ 1969
>(Nature) and continue to the present review soon to be published.

Sounds very interesting!

I found

Nature. 1969 Jun 28;222(200):1263-4.
Transduction mechanism in olfaction and gustation.
Norris DM.

Is this one of the citations you are referring to?

Could you send a few more key citations so I can understand better?

Cheers,
Dan.

>
>dmn
>
>
>----- Original Message ----- 
>From: "Dan Bolser" <dmb at mrc-dunn.cam.ac.uk>
>To: <bio_bulletin_board at bioinformatics.org>
>Sent: Friday, July 02, 2004 3:57 AM
>Subject: Re: [BiO BB] Getting PDB id from Swissprot entry
>
>
>> 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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