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Biocatalysis

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Computational Tools Applied to Enzyme Design − a review

Fernando García-Guevara
  • Corresponding author
  • Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, CP 62210, Cuernavaca, Morelos, México
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Mayra Avelar
  • Corresponding author
  • Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, CP 62210, Cuernavaca, Morelos, México
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Marcela Ayala
  • Corresponding author
  • Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, CP 62210, Cuernavaca, Morelos, México
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Lorenzo Segovia
  • Corresponding author
  • Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, CP 62210, Cuernavaca, Morelos, México
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-02-02 | DOI: https://doi.org/10.1515/boca-2015-0009

Abstract

The protein design toolbox has been greatly improved by the addition of enzyme computational simulations. Not only do they warrant a more ambitious and thorough exploration of sequence space, but a much higher number of variants and protein-ligand systems can be analyzed in silico compared to experimental engineering methods. Modern computational tools are being used to redesign and also for de novo generation of enzymes. These approaches are contingent on a deep understanding of the reaction mechanism and the enzyme’s three-dimensional structure coordinates, but the wealth of information produced by these analyses leads to greatly improved or even totally new types of catalysis.

Keywords: protein engineering; enzyme design; molecular dynamics; quantum mechanics

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About the article

Received: 2015-08-11

Accepted: 2015-11-10

Published Online: 2016-02-02


Citation Information: Biocatalysis, Volume 1, Issue 1, Pages 109–117, ISSN (Online) 2353-1746, DOI: https://doi.org/10.1515/boca-2015-0009.

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© 2015 Fernando García-Guevara, et al.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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