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Subject: Re: [Gnu-darwin-distribution] a csd alternative - msg#00026List: science.chemistry.blue-obeliskP. 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, proclus-x7PKJuapCgi0fEd0lbWiZA@xxxxxxxxxxxxxxxx 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-1MXgZGmSEouYropViTRrB8edHCjMHISts0AfqQuZ5sE@xxxxxxxxxxxxxxxx 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 Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 Thread at a glance:
Previous Message by Date: click to view message previewCrystalEye - Re: a csd alternativeI replied to Michael/Proclus on a different hread before I read BO as follows: This might as well act as a pre-formal announcement for CrystalEye. We see this as a rich source of accurate fragments for 3D molecular building Michael, This has come my way through CCP4BB. You are welcome to the coordinates from WWMM as long as you acknowledge source. It was slightly pre-CC licenses but they should impicitly carry CC-BY. The WWMM molecules are slightly difficult to extract en masse as the metadata are fully exposed by require a link to the data so you have to write a simple script. This was not anticipated when we first put them in. You may also be interested in http://wwmm.ch.cam.ac.uk/crystaleye which aggregates structures from the current crystallographic literature with complete metadata. There is a also a 2D image autogenerated by CDK. You mention "image" - I suspect you mean 3D image but 2D are also important. We shall be extracting ca 30K structures/year in this way and we have a significant back archive. We would hesitate to use the term "CSD alternative" for CrystalEye - it does things that CSD does not do and vice versa. For example it is not comprehensive, but it is Open and creates/allows derivative works. We expect to create a search interface fairly soon probably based on RDF. P. At 19:12 18/05/2007, proclus-x7PKJuapCgi0fEd0lbWiZA@xxxxxxxxxxxxxxxx wrote: 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 <rguha-GZvvpLG7cYSVc3sceRu5cw@xxxxxxxxxxxxxxxx> > 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------ _______________________________________________ Blue-obelisk mailing list Blue-obelisk-1MXgZGmSEouYropViTRrB8edHCjMHISts0AfqQuZ5sE@xxxxxxxxxxxxxxxx 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 Next Message by Date: click to view message previewJumbo 5.4 beta 1 releaseHi all, I'm pleased to announce that 5.4 beta 1 has finally been released (sorry for the delay) and is available from the sourceforge site. Development on Jumbo's trunk is now version 5.5. 5.4b1 has been moved to a branch for bug fixes, and 5.4 will be released when the bugs die off. From the release report: - There is new and improved functionality in MoleculeTool, CrystalTool and ValencyTool thanks to developments on the CrystalEye project. We introduce CMLFragment which supports Markush and polymer structures. This release introduces a new version of schemagen that builds independently of jumbo and hence removes the bootstrapping problems with 5.3. Note however that jumbo is tightly coupled to a particular schema (here, 2.2). The conversion tools in the legacy2cml have been refactored into a separate release (coming soon...) in order to reduce the number of dependencies caused by the core code. Best regards, jim Previous Message by Thread: click to view message previewCrystalEye - Re: a csd alternativeI replied to Michael/Proclus on a different hread before I read BO as follows: This might as well act as a pre-formal announcement for CrystalEye. We see this as a rich source of accurate fragments for 3D molecular building Michael, This has come my way through CCP4BB. You are welcome to the coordinates from WWMM as long as you acknowledge source. It was slightly pre-CC licenses but they should impicitly carry CC-BY. The WWMM molecules are slightly difficult to extract en masse as the metadata are fully exposed by require a link to the data so you have to write a simple script. This was not anticipated when we first put them in. You may also be interested in http://wwmm.ch.cam.ac.uk/crystaleye which aggregates structures from the current crystallographic literature with complete metadata. There is a also a 2D image autogenerated by CDK. You mention "image" - I suspect you mean 3D image but 2D are also important. We shall be extracting ca 30K structures/year in this way and we have a significant back archive. We would hesitate to use the term "CSD alternative" for CrystalEye - it does things that CSD does not do and vice versa. For example it is not comprehensive, but it is Open and creates/allows derivative works. We expect to create a search interface fairly soon probably based on RDF. P. At 19:12 18/05/2007, proclus-x7PKJuapCgi0fEd0lbWiZA@xxxxxxxxxxxxxxxx wrote: 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 <rguha-GZvvpLG7cYSVc3sceRu5cw@xxxxxxxxxxxxxxxx> > 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------ _______________________________________________ Blue-obelisk mailing list Blue-obelisk-1MXgZGmSEouYropViTRrB8edHCjMHISts0AfqQuZ5sE@xxxxxxxxxxxxxxxx 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 Next Message by Thread: click to view message previewJumbo 5.4 beta 1 releaseHi all, I'm pleased to announce that 5.4 beta 1 has finally been released (sorry for the delay) and is available from the sourceforge site. Development on Jumbo's trunk is now version 5.5. 5.4b1 has been moved to a branch for bug fixes, and 5.4 will be released when the bugs die off. From the release report: - There is new and improved functionality in MoleculeTool, CrystalTool and ValencyTool thanks to developments on the CrystalEye project. We introduce CMLFragment which supports Markush and polymer structures. This release introduces a new version of schemagen that builds independently of jumbo and hence removes the bootstrapping problems with 5.3. Note however that jumbo is tightly coupled to a particular schema (here, 2.2). The conversion tools in the legacy2cml have been refactored into a separate release (coming soon...) in order to reduce the number of dependencies caused by the core code. Best regards, jim Loading Comments...
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