[BiO BB] Getting PDB id from Swissprot entry
dmnunif at charter.net
Sat Jul 3 11:08:41 EDT 2004
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.
----- 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:
> >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?
> >----- 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
> >> >to a particular Swissprot id ?
> >> I would use the MSD database, which maintains a manually curated
> >> 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
> >> however, you can consider very close homologues to the above set as
> >> 'solved'. Where you draw the line is a matter of requirement, but you
> >> get reasonable models (allegedly) at > 40% sequence identity, or
> >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY
> >> example).
> >> It all depends on what you want to do.
> >> >Thank you very much..
> >> >
> >> >Regards,
> >> >Sourangshu.
> >> >
> >> >
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