Re: [Blue-obelisk] a csd alternative
On 18 May, Rajarshi Guha wrote: > Will these be 2D structure diagrams? Or ray traced 3D images? If the > former what is the need to store these? They could be easily > generated on the fly (either by local software or by web services > such as http://rguha.ath.cx:8080/cdkws/services/StructureDiagram? > wsdl). If the latter, what is the utility of static 3D images (apart > from the eye-candy aspect) Quick access in the browser window is the answer, accessible to anyone without special configuration. I haven't decided on line v. rendered diagrams. Maybe both. > You can get 3D coordinates for most of PubChem from http:// > www.chembiogrid.org/cheminfo/p3d - depending on the mode of access > (such as bulk downloads) you can get access to the underlying > database if needed. Thanks for the suggestions! Regards, Michael L. Love > --- > Rajarshi Guha <[EMAIL PROTECTED]> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > --- > A sine curve goes off to infinity, or at least the end > of the blackboard. > -- Prof. Steiner > -- 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-- pgpbN8AxH1pmf.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
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/ >> >> >> >> >>-- >>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] GNU-Darwin: the wikipedia credibilty problem
Should Schools Block Sites Like Wikipedia? http://ask.slashdot.org/article.pl?sid=07/04/13/2018210 Stories like this annoy me greatly. From a professional point of view, I find the chemical and biochemical information in Wikipedia to be very credible and useful at this time. Many scientists contribute to the archive, and they take some pains to help assure that the information there is accurate. There are countless examples of groups that are engaged in such activity. I am similarly impressed with most of the information that is provided on other topics as well. In my opinion Wikipedia should be given all the weight of any source in the public press... perhaps more. As always, please feel free to forward this along as you like. 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-- pgpnqtyEjeFDc.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 BODR project on SF?
On 7 Feb, Jerome Pansanel wrote: > > I have been thinking of simply setting up a SF project for just the BODR > > project. Now that it is entering the first Linux distribution (Debian), and It is advantageous for a project to maintain its own site, which can be listed as the main page at the SF. SF is a publicly accessible archive, which is large, stable, and frequently used. It probably is a good place to put your code, if you want it to endure in the public view, although it is also important not to over-rely on it, because it is a private corporation with the associated risks. If a project has the resources, it should maintain its own separate access points in addition to those provided by SF, and use old-fashioned conventional mirror agreements too. Overall, I think that SF listing is a plus for BODR. 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-- pgpa2lJjbBTPg.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
[Blue-obelisk] FWD: Salon magazin: Science publishers get stupid
Thanks for the heads up. I am glad that we are a little out in front on this, and we will definitely be staying on it. It was a good read to see what may be coming from the other side. Please pass this along as you see fit. 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 31 Jan, Tobias Kind wrote: > Hi, > Nature Journal has learned that a group of scientific publishers, > including Elsevier, Wiley and the American Chemical Society > has hired Eric Dezenhall aka the "PR pit bull" to take on the > free-information > movement, which campaigns for scientific results to be > made freely available. Happily we have the NIH, that asked all researchers > that it funds to send copies of research results to the open access PubMed. > > > Nature: PR's 'pit bull' takes on open access > http://www.nature.com/nature/journal/v445/n7126/pdf/445347a.pdf > > Spiegel: Papierimperium hetzt gegen freies Web > http://www.spiegel.de/wissenschaft/mensch/0,1518,462845,00.html > > Salon: Science publishers get stupid > http://www.salon.com/tech/htww/2007/01/25/free_information/index.html > > > I also wonder why european research has such a low impact > on the open-access movement compared to the US. > Don't get me wrong, I am not talking about small or large projects (CDK), > I am not talking about the few people who did so much for Open Access. > I talk about a general "lead" a "decision" stuff that gets "done". > > Where is PubChem coming froom, where is PubMed coming from. > where is the NCI database coming from, where is ChemIDPlus coming from, > where is PLOS (Public Library of Science) coming from? > Of course this is purely based on a chemistry view. > And yes BioMed Central is UK based, compare that to the list above. > > You would expect such huge and respected organizations > like the Max-Planck-Society step forward and take a *lead* > towards open access. But? Nothing. > > The Open Access EU petition for guaranteed public access > to publicly-funded research? Its a petition, nothing else. > Lets face it, open-access to research results will come > sonner or later, open-access to data obtained from research > will come sooner or later, but it could be much qicker :-) > > ...to make sure, I was "wondering", I am not starting > a flame-war, the only thing I am doing for OA sofar is, that I > try to publish in OA journals, thats very little compare to > others. > > Dr. Tobias Kind > UC Davis Genome Center > Metabolomics Group > > http://fiehnlab.ucdavis.edu/ > Tel:+1-530-754-7113 > > > > ___ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- 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-- pgp61IwEI9mTh.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
On 19 Dec, peter murray-rust wrote: > 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 What is pm3? I noticed that the coordinate files are stored in cml format, which we can presumably translate to pdb for our needs with Open Babyl. 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/ > 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-- pgpHJFneC8MfQ.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
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
[Blue-obelisk] a csd alternative
I would like to recommend the following alternatives to the csd suite for chemical database searches. 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/ 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-- pgpOVxB9LO2iD.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
