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Automated molecule editing in molecular design

  • Perspective
  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

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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Authors and Affiliations

  1. Grupo de Estudos em Química Medicinal (NEQUIMED), Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil

    Peter W. Kenny, Carlos A. Montanari, Igor M. Prokopczyk, Fernanda A. Sala & Geraldo Rodrigues Sartori

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  1. Peter W. Kenny
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  2. Carlos A. Montanari
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  3. Igor M. Prokopczyk
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Correspondence to Peter W. Kenny.

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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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