In Silico-Directed Evolution Using CADEE

Amrein, BA and Runthala, A and Kamerlin, SCL (2019) In Silico-Directed Evolution Using CADEE. [Book Chapter]

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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.

Item Type:	Book Chapter
Publication:	Methods in Molecular Biology
Publisher:	Humana Press Inc.
Additional Information:	The copyright for this article belongs to Humana Press Inc.
Keywords:	enzymology; simulation; workflow; biology; chemistry; directed molecular evolution; genetics; procedures; protein engineering, enzyme, Computational Biology; Directed Molecular Evolution; Enzymes; Protein Engineering
Department/Centre:	Division of Mechanical Sciences > Civil Engineering
Date Deposited:	29 Nov 2022 05:21
Last Modified:	29 Nov 2022 05:21
URI:	https://eprints.iisc.ac.in/id/eprint/78043

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