[BiO BB] Getting PDB id from Swissprot entry

Sun Jul 4 00:54:00 EDT 2004

Hi Dan:

I shall provide you with a sizeable list of references tomorrow; it is too
late now. Oh, heck, here are a few.

You could start with:
1) Norris.1985. Bioelectrochemistry and Bioenergetics 14: 449 - 456.

2)Rozental & Norris. 1973 . Nature 244: 370 - 371.

3)Norris, et al. 1970. Science 170: 754 - 755.

4) Norris, et al. 1976. Comp. Biochem. Physiol. 57C: 55 - 59.

5) Norris.1971. Experientia 27: 531 -532.

6) Singer, et al. 1975. Nature 256: 222 - 223.

Extensive reviews of our work to the time:

Norris, D. M. 1986. Anti-feeding compounds, pp. 97 - 146, in G. Haug and H.
Hoffmann (eds.) Chemistry of Plant Protection. 1. Springer-Velag, Berlin.

Norris, D. M. (ed). 1981. Perception of Behavioral Chemicals. Elsevier /
North-Holland Biomedical Press, Amsterdam.

Etc.

Norris, D.M., and I. Markovic.2003.  Tritrophic interactions: The inducible
defenses of plants, pp: 87 - 109, in O. Koul and G. S. Dhaliwal (eds.).
Predators and Parasitoids, Taylor & Francis, London & New York.

See you tomorrow.

dmn

----- Original Message ----- 
From: "Dan Bolser" <dmb at mrc-dunn.cam.ac.uk>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Saturday, July 03, 2004 11:39 AM
Subject: Re: [BiO BB] Getting PDB id from Swissprot entry

> 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.
> >> >> >
> >> >> >
> >> >>
> >> >> _______________________________________________
> >> >> 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
> >> >
> >>
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> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> >
> >
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> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
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