Machine Learning in Enzyme Engineering

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Enzyme engineering is the process of customizing new biocatalysts with improved properties by altering their constituting sequences of amino acids. Despite the immensity of possible alterations, this procedure has already yielded remarkable results in new designs and optimization of enzymes for chemical and pharmaceutical biosynthesis, regenerative medicine, food production, waste biodegradation and biosensing.(1 The two established and widely used enzyme engineering strategies are rational design(5,6) and directed evolution.(7,8) The former approach is based on the structural analysis and in-depth computational modeling of enzymes by accounting for the physicochemical properties of amino acids and simulating their interactions with the environment. The latter approach takes after the natural evolution in using mutagenesis for iterative production of mutant libraries, which are then screened for enzyme variants with the desired properties. These two strategies may naturally complement each other: e.g., site-directed or saturation mutagenesis may be applied on the rationally chosen hotspots.(9)