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In Silico-Directed Evolution Using CADEE

  • Beat Anton Amrein
  • Ashish Runthala
  • Shina Caroline Lynn Kamerlin
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1851)

Abstract

Recent years have seen an explosion of interest in both sequence- and structure-based approaches toward in silico-directed evolution. We recently developed a novel computational toolkit, CADEE, which facilitates the computer-aided directed evolution of enzymes. Our initial work (Amrein et al., IUCrJ 4:50–64, 2017) presented a pedagogical example of the application of CADEE to triosephosphate isomerase, to illustrate the CADEE workflow. In this contribution, we describe this workflow in detail, including code input/output snippets, in order to allow users to set up and execute CADEE simulations on any system of interest.

Key words

Enzyme design Directed evolution Computational enzymology Computational enzyme design Empirical valence bond 

Notes

Acknowledgments

The European Research Council provided financial support under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 306474. SCLK would also like to thank the Knut and Alice Wallenberg Foundation and the Royal Swedish Academy of Sciences for a Wallenberg Academy Fellowship, and the Swedish Research Council for providing support through project grant 2015-04928. All calculations were performed on the Abisko cluster at the HPC2N center in Umeå and on the Triolith cluster at the NSC in Linköping, thanks to a generous supercomputing allocation provided by the Swedish National Infrastructure for Computing (SNIC grant 2015/16-12). In addition, we would like to thank Arina Gromova for extensive testing of CADEE, Fabian Steffen-Munsberg for initial testing, and Miha Purg for helpful discussions about qscripts/qtools.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Beat Anton Amrein
    • 1
  • Ashish Runthala
    • 3
  • Shina Caroline Lynn Kamerlin
    • 2
  1. 1.Associate Scientist, Tecan Schweiz AGMännedorfSwitzerland
  2. 2.Department of ChemistryBMC, Uppsala UniversityUppsalaSweden
  3. 3.Indian Institute of ScienceBangaloreIndia

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