Hi Geoff, I completely agree, it is also important to have full reactions stored because they allow you to calculate, e.g., physico-chemical parameters from the full molecule structures of know reactions (which might be helpful to estimate whether the reaction will run - well, this would be for the later stage of the project ;-) ).
But for retrosynthesis analysis I think you need something more general than full reactions, i.e. SMIRKS. I also agree that both sides, a open reaction repository and a open SMIRKS repository for (retro)reactions would have an enormous potential. I emphasize "open" because all commercial efforts on retrosynthesis kind of stalled - and most reaction databases are closed which is also unfortunate. Best, Markus On 7/24/2012 12:52 PM, Geoff Hutchison wrote: >> Putting together a Open Reaction Database is probably a really >> good idea, however - although closely related, of course - for retro- >> synthesis analysis you might alternatively put together a collection >> of SMARTS and SMIRKS patterns > > Ideally, such a reaction database would be in SMIRKS. (IIRC, SMIRKS is a > superset of reaction SMARTS, so you wouldn't need "SMARTS" per-se -- they're > already part of the SMIRKS.) While it's fairly easy to generate reaction > SMILES (e.g., using Open Babel) for specific reactions, generating the SMIRKS > would be a bit harder. > > This is one reason I've been pushing for OSRA and ChemDraw files, since > academic instructors could probably be talked into giving up lecture notes > with general reaction schemes. > > I think there would be *lots* of interesting applications. It looks like Abe > has made a database from the patent literature, but I don't know if it's yet > available in file form: > http://nar.oxfordjournals.org/content/40/D1/D428 > http://dcv.uhnres.utoronto.ca/SCRIPDB/search/ > > Cheers, > -Geoff > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Markus Sitzmann, Ph.D. Chemical Biology Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health 376 Boyles St Frederick, MD 21702, USA 301-846-5974 (office) 301-846-6033 (fax) sitzm...@helix.nih.gov http://www.linkedin.com/pub/1/7b8/342 http://www.xing.com/profile/Markus_Sitzmann ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
