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 -- 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-- pgp5NLYvQwiHg.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 May 18, 2007, at 1:34 PM, [EMAIL PROTECTED] wrote: 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 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)? 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. --- 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 ___ 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
[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
