Subject: Re: [Gnu-darwin-distribution] a csd alternative



Was this mail meant to go to the Blue Obelisk list? I don't know who it is from (we like to know the names, not just initials, of posters) and it doesn't follow the thread. Also it was crossmailed to two other lists.

P.


At 23:44 20/05/2007, m.m.w wrote:
Hi Mike,

can i forward to Institut Pasteur and CNRS-GIF ?

last year, i also met a guy from CEA Grenobles, who worked on
Molecular DB
he asked me some "advise" about DB Object Design , maybe it's an
another way to explore ...

-mmw

I would like to create an online archive of images of all the small
molecules that are available from WorldWideMolecularMatrix and other
sources that provide molecular coordinates.

http://www.dspace.cam.ac.uk/handle/1810/724

Some notes and links about the molecules could also be provided. Not
only would such an archive be immensely useful for many researchers
(including myself), but it could also provide the raw material for
Wikipedia stubs and other projects. I have a dual core Opteron at
gnu-darwin.org that is currently mostly idle at this time, and I would
really like to do this. I am familiar with the necessary molecular
coordinate formatting, rendering, image processing, and other software
that is required to do the project. Any suggestions on how to get the
required level of access to the molecular databases in order to get
this
done would be much appreciated. BTW, obviously we are talking free
and
open public access here.

How does http://molecules.gnu-darwin.org/ sound?

Please send me links to other small molecule coordinate archives, so
that I can get started right away. There are a few listed below too.

BTW, if someone has already done this, why is it not in Google, and
please point me to it. Thanks!

Regards,
Michael L. Love Ph.D
Department of Biophysics and Biophysical Chemistry
School of Medicine
Johns Hopkins University
725 N. Wolfe Street
Room 608B WBSB
Baltimore MD 21205-2185
Interoffice Mail: 608B WBSB, SoM

office: 410-614-2267
lab: 410-614-3179
fax: 410-502-6910
cell: 443-824-3451
http://www.gnu-darwin.org/


On 19 Dec, peter murray-rust wrote:

At 17:16 18/12/2006, [email protected] wrote:



I assume this mail came from Blue Obelisk - the header iws confused.




I would like to recommend the following alternatives to the csd
suite
for chemical database searches.

What is meant by csd? If this is the Cambridge Database then this
primarily only relevant if the alternative sources contains
crystallographic data.



These are open databases of chemical
substances, which you might find bound in your crystals as
substrates or
ligands. The databases can be downloaded in whole, or they are
tied in
to PubChem, thus conforming to the principle of public
accessibility.
Here are the links

http://chembank.broad.harvard.edu/

What are the license conditions on this. It is not available without
registering. And can the whole database be downloaded without further
permission?


http://biocyc.org/open-compounds.shtml

I learned about these tools on the Blue-obelisk list, which is
dedicated to FOSS tools in chemistry. Some of these folks are
working on the Wikipedia chemical specification formats or they have
agreed to do their scientific work in an open data-sharing
environment.
Nice work to them!

Regards,
Michael L. Love Ph.D
Department of Biophysics and Biophysical Chemistry
School of Medicine
Johns Hopkins University
725 N. Wolfe Street
Room 608B WBSB
Baltimore MD 21205-2185

Interoffice Mail: 608B WBSB, SoM

office: 410-614-2267
lab: 410-614-3179
fax: 410-502-6910
cell: 443-824-3451
http://www.gnu-darwin.org/




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Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road, Cambridge CB2 1EW, UK
+44-1223-763069

Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
University of Cambridge,
Lensfield Road, Cambridge CB2 1EW, UK
+44-1223-763069




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