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.
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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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Amrein, B.A., Runthala, A., Kamerlin, S.C.L. (2019). In Silico-Directed Evolution Using CADEE. In: Sikosek, T. (eds) Computational Methods in Protein Evolution. Methods in Molecular Biology, vol 1851. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8736-8_22
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DOI: https://doi.org/10.1007/978-1-4939-8736-8_22
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