On 24 January 2011 14:28, Daniel Zaharevitz <zahar...@mail.nih.gov> wrote:
> Thanks for the info. I think I need to put together a few detailed examples, > but unfortunately I'll be busy for a few days. Anyway, I think part of it is > related to what we talked about in Cambridge: how do we "clean up" structure > representations to make sure we understand how the tools will behave. > > To give the list the context: At DTP we accept molecules for testing in the > Human Tumor Cell Line Screen (NCI-60) ; see > http://dtp.nci.nih.gov/docs/misc/common_files/submit_compounds.html. Our > biggest criterion for acceptance is structure novelty. As it stands now the > only way you can find out if a structure you are submitting is novel to our > program is to submit it and wait to hear back from us. Our open compounds > are freely available so you could set a search through those, but about half > our compounds are confidential, so that doesn't completely solve the > problem. I want to set up a web service that will accept a structure and > return the highest tanimoto from all of our structures. That way submitters > can check their structures before submitting (or maybe even synthesizing) > and not waste time on a 2-3 day submission response turnaround. Any > suggestions regarding parameters (like which fp type) to use would be > appreciated. FP2, the default fingerprint, is a Daylight-type fingerprint and would be generally used for this type of thing. It should be noted that it may be possible to recreate the molecule given the fingerprint (I think there was a paper on this a while back), so you want to bear this in mind when dealing with confidential compounds. > DanZ > > > > > /******************************************** > * Daniel Zaharevitz > * Chief, Information Technology Branch > * Developmental Therapeutics Program > * National Cancer Institute > * zahar...@mail.nih.gov > * > ********************************************/ > > > > ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
