On Feb 1, 2011, at 12:34 PM, Imran Haque wrote: > On 02/01/2011 05:37 AM, Daniel Zaharevitz wrote: >> We will be >> looking to find a set of fingerprints that >> 1) never (or as close to never as we can get) return a value of 1.0 >> for different structures. > > I'm not sure that's it's implemented in OpenBabel, but if it's a 2D > structural descriptor you want, you could give LINGO (Vidal, Thormann, > and Pons, JCIM 2005; DOI: 10.1021/ci0496797) a shot. I've written a > LINGO implementation that's primarily targeted at GPUs but has a > reasonably fast CPU version (https://simtk.org/home/siml). The CPU > code > is not as quick as the fastest DFA-based methods, but it'll handle > your > 9000^2 similarities in a matter of seconds. > > (PS, it's BSD-licensed, in case anyone would like to integrate it > into OB!) > >> 2) has a well behaved (or maybe just well documented) relation >> between >> structure similarity and NCI-60 correlation. I'm not sure what we >> will >> get here, but I would like to be able to say something like a >> similarity score of>0.9 gives a 80% chance of a NCI-60 correlation of >>> 0.6. > > The VTP paper above as well as a later one (DOI: 10.1021/ci6002152) > show > decent correlation with activity; in my experience, similar to any > other > given 2D similarity measure. I'm sure you know this, but "tuning" > fingerprints to any given small dataset is a dangerous art; it's very > easy to overfit. >
Thanks for the interesting and useful pointers. I hope we can give it a try when I get the data together. 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
