protein sequence motif data base?

MICPRF at latvax8.lat.oz MICPRF at latvax8.lat.oz
Thu Aug 23 07:29:01 EST 1990


In article <4609 at latvax8.lat.oz>, MICPRF at latvax8.lat.oz writes:
> I was wondering if anyone has compiled a data base containing the
> motifs characteristic of particular functional domains of proteins -
> eg. the leucine zipper, ATP binding proteins, GTP binding sites on
> GTP binding proteins etc. The nearest thing I know to it is the prosite
> data base, which I have - but is there anything else. Would the prosite
> data base in combination with something like the plsearch programme be
> sufficient to pick up a leucine zipper in a new sequence for example?
> 				Paul Fisher (micprf at latvax8.lat.oz.au)
> P.S. Please post reponses to the news group as this might be of general
> interest.

I am posting a response to my original query as I think it warrants
wider dissemination:

______________________________________________________________________________

In reply to an inquiry from Paul Fisher (micprf at latvax8.lat.oz.au) concerning a
Protein Sequence Motif Data Base:

The NBRF PIR staff has been collecting motif data, and considering the
development of the special format and software that such a data base would
require in order to be useful.  Unfortunately, the present very poor level of
funding from the NIH, and their apparent reluctance to fund the development new
databases, has prevented us from advancing beyond this planning stage.  We hope
that U.S. researchers will let us know of their interest in a motif database
useable in conjuction with the PIR.  Assessing the demand for such a database
would help us choose whether to proceed with this project and determine how
best to obtain funding for it.
------------------------------------------------------------------------
GARAVELLI at GUNBRF.BITNET          Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007



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