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Modeling Chemical Diversity

  • Pablo Carbonell
Chapter
Part of the Learning Materials in Biosciences book series (LMB)

Abstract

In this chapter, you will learn about ways for modeling the chemical diversity found in metabolic pathways in nature. Organisms have evolved enzymes, i.e., specialized proteins to carry out chemical transformations that produce the compounds required for life. We have nowadays a good understanding about the mechanisms of natural evolution that allowed the creation of new enzymes and new activities. We are going to model and simulate such behavior by encoding reactions in the same way as we encode a language using words. This will allow us to understand the grammar behind the generation of new reactions. Even more interestingly, we will see how the grammar can be potentially used to enumerate any possible reaction and any possible compound that can be produced in nature. At the end of this chapter, we should have gained a good understanding of the biochemical space that exists in nature.

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Further Reading

  1. A good introduction to biocatalysis:Google Scholar
  2. Grunwald, P.: Biocatalysis. Biochemical Fundamentals and Applications. Imperial College Press (2009)CrossRefGoogle Scholar
  3. An interesting discussion on enzyme promiscuity and evolution:Google Scholar
  4. Khersonsky, O., Tawfik, D.S.: Enzyme promiscuity: a mechanistic and evolutionary perspective. Ann. Rev. Biochem. 79(1), 471–505 (2010)CrossRefGoogle Scholar
  5. Useful introductions to chemoinformatics and associated algorithms can be found in:Google Scholar
  6. Judson, P.: Knowledge-Based Expert Systems in Chemistry. Theoretical and Computational Chemistry Series. Royal Society of Chemistry, Cambridge (2009)Google Scholar
  7. Gasteiger, J., Engel, T. (eds.): Chemoinformatics. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG (2003)Google Scholar
  8. Faulon, J.L., Bender, A.: Handbook of Chemoinformatics Algorithms. Chapman & Hall/CRC (2010)Google Scholar
  9. More details about the implementation of chemoinformatics algorithms are available at the sites for the software packages:Google Scholar
  10. The RDKit Python library: http://rdkit.org
  11. The CDK [ 9] Java library: https://cdk.github.io/
  12. An insightful discussion about chemical space enumeration:Google Scholar
  13. Reymond, J.L., Ruddigkeit, L., Blum, L., van Deursen, R.: The enumeration of chemical space. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2(5), 717–733 (2012)Google Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Pablo Carbonell
    • 1
  1. 1.Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK

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