Dear Soeren, On Wed, Apr 6, 2011 at 1:28 PM, Sören Wacker <[email protected]> wrote: > > I am wondering whether you can use RDKit for the estimation of > protonation states of chemical compounds, too. > And if yes, how can you do that, and what do you think how reliable it is? > Or is there a way to implement this?
No functionality like this is currently implemented in the RDKit. It's a hard problem. I would guess that it is possible to implement most of the non-quantum-mechanical approaches for pKa estimation, but all of them would require a fair amount of work. Gordon Crippen published a relatively simple pKa estimator for monoprotic molecules a couple of years ago: http://dx.doi.org/10.1021/ci8001815 The SMARTS patterns used in the paper could certainly be translated to work within the RDKit. Best, -greg ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
