Abstract
The ability to modify chemical structures in an automated and controlled manner is useful in molecular design. This Perspective introduces the MUDO molecule editor and shows how automated molecule editing can be used to standardize structures, enumerate tautomeric and ionization states, identify matched molecular pairs. Unlike its predecessor Leatherface, MUDO can also process 3D structures and this capability can be used to link non-covalently docked ligands to proteins.





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Acknowledgments
We are grateful to the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; Grant Numbers #2011/01893-3 and #2011/20572-3)) and the Conselho Nacional de Pesquisa (CNPq) for financial support. We thank OpenEye for an academic software license and the two anomymous reviewers for their helpful and constructive comments.
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Kenny, P.W., Montanari, C.A., Prokopczyk, I.M. et al. Automated molecule editing in molecular design. J Comput Aided Mol Des 27, 655–664 (2013). https://doi.org/10.1007/s10822-013-9676-0
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DOI: https://doi.org/10.1007/s10822-013-9676-0