Re: [Blue-obelisk] a csd alternative
At 15:17 19/12/2006, [EMAIL PROTECTED] wrote: On 19 Dec, peter murray-rust wrote: > What is meant by csd? If this is the Cambridge Database then this > primarily only relevant if the alternative sources contains > crystallographic data. For our purposes I disagree, because a chemical crystallographic structure is not necessary. In practice, an idealized chemical structure can be fitted within a new protein crystal structure just as well. If what you meant is "can we have an open database of 3D structures, the answer is a qualified 'yes'" - without taking them from CSD. There are two main methods: * extract them from non-copyright crystal structures (there are a lot of these and we are collating them - watch this space. * create them from connection tables. There are various levels of "accuracy" including forcefields and theochem methods. We have done this for 200,000 molecules - see http://www.dspace.cam.ac.uk/handle/1810/724 If you are happy with PM3, then use these P. Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] Visualizing Cheminformatics Algorithms
I am returning to this old thread. Steve Bachrach just let me know
that the Internet Journal of Chemistry is up again! So if somebody is
interested in checking our applet illustrating various selection
algorithms, here it is:
http://www.ijc.com/articles/1999v2/14/
(and be forgiving, Java 1.0 in 1999 was slightly different from the
language we are using now :-).
peter
On 11/20/06, Peter Ertl <[EMAIL PROTECTED]> wrote:
Unfortunately I do not have the publication any more. It disappeared
sometimes during several mergers and transfers I participated in. And
I was too careless to archive myself.
I contacted both Steves (Bachrach and Heller) who were responsible for
the IJC, hopefully they provide some info about the future of IJC and
maybe even possibility to recover the paper.
Nice greetings,
p
On 11/18/06, richard apodaca <[EMAIL PROTECTED]> wrote:
>
> --- Christoph Steinbeck <[EMAIL PROTECTED]>
> wrote:
>
> > Peter Ertl wrote:
> > > The article features (or better featured, the IJC
> > site seems to be
> > > dead) a nice applet allowing people to run
> > interactively various types
> > > of diversity selection algorithm and compare the
> > results.
>
> BTW, Peter, if you still have a copy of the article,
> I'd really be interested in one.
>
> > > As I said, the IJC site is now dead. Maybe this is
> > one reason why
> > > authors do not trust too much the new open access
> > journals. Which of
> > > them will be alive in 10 years?
> >
> > Peter,
> >
> > thanks a lot for contributing to the Blue-Obelisk
> > List :-)
> >
> > I can only second what Rich already replied. Open
> > Access *is* the model of the
> > future since it gives us back the rights for our
> > work.
> >
> > The problem with disappearing content is also one of
> > the regular publishers -
> > where are their archives going when they die. It's
> > just a question of likelihood
> > of dying :-)
> >
> > Also, I think, it is a responsibility of societies
> > (as in: all the people in
> > Germany) to make sure their knowledge doesn't die.
> > Certainly if they consider
> > themselves to be a "Wissensgesellschaft" ("knowledge
> > societies").
> >
> > One way towards this is putting things in
> > institutional repositories - the
> > University of Cologne has a much higher likelihood
> > of being around in 100 years
> > than any of the regular publisher that I know.
> >
> > A second way is national libraries and their
> > archival initiatives. The German
> > National Library is now required by law to archive
> > whatever appeares on the net
> > in Germany (Within certain boundaries, but
> > scientific articles certainly are
> > part of this mission).
>
> Also the private sector. A sustainable business model
> has yet to be developed. But then again, that's what
> they uesed to say about Google.
>
> > On remark at the end: the fact that the IJC site is
> > down and that the archive
> > has not been made accessible somewhere else is
> > *very* depressing.
> >
> > Cheers,
> >
> > Christoph
> >
> > --
> > PD Dr. Christoph Steinbeck
> > ([EMAIL PROTECTED])
> > Head of the Research Group for Molecular Informatics
> > Cologne University BioInformatics Center
> > (http://almost.cubic.uni-koeln.de)
> > Zülpicher Str. 47, 50674 Cologne
> > Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
> >
> >
>
>
>
> Richard Apodaca
> Blog: http://depth-first.com
>
>
>
>
> Sponsored Link
>
> Mortgage rates near 39yr lows.
> $310k for $999/mo. Calculate new payment!
> www.LowerMyBills.com/lre
>
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Re: [Blue-obelisk] a csd alternative
On 19 Dec, peter murray-rust wrote: > What is meant by csd? If this is the Cambridge Database then this > primarily only relevant if the alternative sources contains > crystallographic data. For our purposes I disagree, because a chemical crystallographic structure is not necessary. In practice, an idealized chemical structure can be fitted within a new protein crystal structure just as well. >>http://chembank.broad.harvard.edu/ > > What are the license conditions on this. It is not available without > registering. And can the whole database be downloaded without further > permission? I would be interested in hearing the answer to this question from the other members of the list as well. Obviously, I feel that full access is best. Regards, Michael L. Love Ph.D Department of Biophysics and Biophysical Chemistry School of Medicine Johns Hopkins University 725 N. Wolfe Street Room 608B WBSB Baltimore MD 21205-2185 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab:410-614-3179 fax:410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ >>Blue-obelisk mailing list >>Blue-obelisk@hardly.cubic.uni-koeln.de >>http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk > > Peter Murray-Rust > Unilever Centre for Molecular Sciences Informatics > University of Cambridge, > Lensfield Road, Cambridge CB2 1EW, UK > +44-1223-763069 -- Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- pgppQCIEbaD7U.pgp Description: PGP signature ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
Re: [Blue-obelisk] a csd alternative
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/ -- Visit proclus realm! http://proclus.tripod.com/ -BEGIN GEEK CODE BLOCK- Version: 3.1 GMU/S d+@ s: a+ C UBULI$ P+ L+++() E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e h--- r+++ y --END GEEK CODE BLOCK-- ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 ___ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
