DOE OSTI · 3398691
Artificial intelligence tools for enzyme engineering and metabolic engineering
Abstract
Enzyme engineering and metabolic engineering drive innovation in energy biotechnology. In recent years, artificial intelligence (AI) has supported successful applications in designing effective enzymes and productive microbial cell factories. This review summarizes recent advances in enzyme redesign using protein language models, de novo enzyme design with generative models, and AI tools for engineering metabolism and related cellular phenotypes. Across these areas, AI models are shifting from single modality inputs to integrated representations of protein function, metabolic pathways, and cell states. We emphasize that unifying the diverse data representations across scales will be necessary for advancements in energy biotechnology.
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Volk, Michael [Univ. of Illinois at Urbana-Champaign, IL (United States). Carl R. Woese Institute for Genomic Biology; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)], Kaushik Pillalamarri, Vishal [Univ. of Illinois at Urbana-Champaign, IL (United States). Carl R. Woese Institute for Genomic Biology; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States); Univ. of Illinois at Urbana-Champaign, IL (United States). Center for Biophysics and Quantitative Biology], Guo, Ruihan [Univ. of Illinois at Urbana-Champaign, IL (United States)], Liu, Ge [Univ. of Illinois at Urbana-Champaign, IL (United States). Carl R. Woese Institute for Genomic Biology; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States); Univ. of Illinois at Urbana-Champaign, IL (United States). NSF Molecule Maker Lab Inst.; Univ. of Illinois at Urbana-Champaign, IL (United States). NSF iBioFoundry], Zhao, Huimin [Univ. of Illinois at Urbana-Champaign, IL (United States). Carl R. Woese Institute for Genomic Biology; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States); Univ. of Illinois at Urbana-Champaign, IL (United States). Center for Biophysics and Quantitative Biology; Univ. of Illinois at Urbana-Champaign, IL (United States). NSF Molecule Maker Lab Inst.; Univ. of Illinois at Urbana-Champaign, IL (United States). NSF iBioFoundry] (ORCID:0000000290696739). 2026-06-03. Artificial intelligence tools for enzyme engineering and metabolic engineering. https://doi.org/10.1016/j.copbio.2026.103522
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