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Classification of Chemical Reactions and Chemoinformatic Processing of Enzymatic Transformations

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Chemoinformatics and Computational Chemical Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 672))

Abstract

The automatic perception of chemical similarities between chemical reactions is required for a variety of applications in chemistry and connected fields, namely with databases of metabolic reactions. Classification of enzymatic reactions is required, e.g., for genome-scale reconstruction (or comparison) of metabolic pathways, computer-aided validation of classification systems, or comparison of enzymatic mechanisms. This chapter presents different current approaches for the representation of chemical reactions enabling automatic reaction classification. Representations based on the encoding of the reaction center are illustrated, which use physicochemical features, Reaction Classification (RC) numbers, or Condensed Reaction Graphs (CRG). Representation of differences between the structures of products and reactants include reaction signatures, fingerprint differences, and the MOLMAP approach. The approaches are illustrated with applications to real datasets.

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Acknowledgments

Diogo A. R. S. Latino acknowledges Fundação para a Ciência e Tecnologia (Ministério da Ciência, Tecnologia e Ensino Superior, Lisbon, Portugal) for financial support under Ph.D. grant SFRH/BD/18347.

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Authors and Affiliations

  1. CQFB and REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal

    Diogo A. R. S. Latino & João Aires-de-Sousa

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  1. Diogo A. R. S. Latino
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  2. João Aires-de-Sousa
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Editors and Affiliations

  1. , Department of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universitä, Dahlmannstr. 2, Bonn, 53113, Germany

    Jürgen Bajorath

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© 2011 Humana Press

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Latino, D.A.R.S., Aires-de-Sousa, J. (2011). Classification of Chemical Reactions and Chemoinformatic Processing of Enzymatic Transformations. In: Bajorath, J. (eds) Chemoinformatics and Computational Chemical Biology. Methods in Molecular Biology, vol 672. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-839-3_13

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  • DOI: https://doi.org/10.1007/978-1-60761-839-3_13

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-838-6

  • Online ISBN: 978-1-60761-839-3

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