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Directed enzyme evolution has proven to be a powerful means to endow biocatalysts with novel catalytic repertoires. Apart from completely random gene mutagenesis, site-directed or site-saturation mutagenesis requires a semi-rational selection of the amino acid positions or the substituted residues, which can dramatically reduce the screening efforts in protein engineering. To this end, in silico prediction methods play a pivotal role in targeting site-saturation mutagenesis. In this chapter, we provide two distinct computational methods, (a) conformational dynamics-guided design and (b) protein-ligand interaction fingerprinting analysis, to identify specific positions for site-saturation mutagenesis toward manipulating substrate specificity/stereoselectivity of an alcohol dehydrogenase, and improving activity of a carboxylic acid reductase, respectively. © 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.


Ge Qu, Zhoutong Sun. In Silico Prediction Methods for Site-Saturation Mutagenesis. Methods in molecular biology (Clifton, N.J.). 2022;2397:49-69

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PMID: 34813059

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