I have never used it, but RDKit has functionality to standardize the representation, as described here: https://bitsilla.com/blog/2021/06/standardizing-a-molecule-using-rdkit/. I couldn't say if either approach is better/worse than the other. With tautomers, my guess is that you have to either be consistent with the representation, or use the tautomeric form that is most relevant to your work. You can use quantum chemistry to calculate the most stable form ( https://pubs.acs.org/doi/10.1021/acs.jcim.0c00232), but even then, the most stable form may not be the most relevant, or the forms may exist in approx. equal proportions, etc.
On Thu, Mar 31, 2022 at 12:57 PM Marawan Hussien via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > Hi, > > I am wondering if anyone has made use (in the form of code, scripts, etc) > of this database to identify canonical tautomers or the most stable > ensemble of tautomers for organic, drug-like molecules: > https://github.com/WahlOya/Tautobase > > The attached reference also looks very very detailed: > > > https://figshare.com/articles/preprint/The_Prediction_of_Tautomer_Preference_in_Aqueous_Solution_Version_1_0_/8966276/1 > > Thanks, > Marawan > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- *Rafael da Fonseca Lameiro * PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED) São Carlos Institute of Chemistry - University of São Paulo - Brazil [image: orcid logo 16px] https://orcid.org/0000-0003-4466-2682
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