[Chimera-users] Tautomer Prediction

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 11 13:48:49 PST 2011

Hi Nancy,
Please remember that the chimera-users list is generally for questions related to Chimera.  CCL.net is more appropriate for this type of question, as mentioned in the responses to your two earlier, very similar questions.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 11, 2011, at 1:12 PM, Nancy wrote:

> Hi All,
> Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value of the acidic hydrogen on the thiazolidinedione ring of pioglitazone is 4.57 (see attached "Figure_1.gif").  Therefore, the predominant species at pH 7.0 predicted by MarvinSketch is the one depicted in "Figure_2.gif".  The different tautomeric forms predicted by MarvinSketch are shown in "Figure_3.gif".
> Can anyone explain where these predictions come from, and if they are correct?  Also, are there other programs that can accurately predict tautomeric forms?
> Thanks,
> Nancy
> <Figure_1.gif><Figure_2.gif><Figure_3.gif>

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