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.
CITATION STYLE
Amrein, B. A., Runthala, A., & Kamerlin, S. C. L. (2019). In Silico-Directed Evolution Using CADEE. In Methods in Molecular Biology (Vol. 1851, pp. 381–415). Humana Press Inc. https://doi.org/10.1007/978-1-4939-8736-8_22
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