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Opportunities and challenges for machine learning-assisted enzyme engineering
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
Automated in vivo enzyme engineering accelerates biocatalyst optimization
Achieving cost-competitive bio-based processes requires development of stable and
selective biocatalysts. Their realization through in vitro enzyme characterization and …
selective biocatalysts. Their realization through in vitro enzyme characterization and …
Generalized biomolecular modeling and design with RoseTTAFold All-Atom
Deep-learning methods have revolutionized protein structure prediction and design but are
presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which …
presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which …
Building enzymes through design and evolution
EJ Hossack, FJ Hardy, AP Green - ACS Catalysis, 2023 - ACS Publications
Designing efficient enzymes is a formidable challenge at the forefront of modern
biocatalysis. Here, we review recent developments in the field and illustrate how the …
biocatalysis. Here, we review recent developments in the field and illustrate how the …
Strategies for designing biocatalysts with new functions
The engineering of natural enzymes has led to the availability of a broad range of
biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and …
biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and …
Protein design using structure-prediction networks: AlphaFold and RoseTTAFold as protein structure foundation models
Designing proteins with tailored structures and functions is a long-standing goal in
bioengineering. Recently, deep learning advances have enabled protein structure …
bioengineering. Recently, deep learning advances have enabled protein structure …
Artificial metalloenzymes
T Vornholt, F Leiss-Maier, WJ Jeong… - Nature Reviews …, 2024 - nature.com
The development of artificial metalloenzymes (ArMs) aims to expand the capabilities of
enzymatic catalysis, most notably towards new reaction mechanisms. Frequently, ArMs …
enzymatic catalysis, most notably towards new reaction mechanisms. Frequently, ArMs …
Recent advances in the design and optimization of artificial metalloenzymes
Embedding a catalytically competent transition metal into a protein scaffold affords an
artificial metalloenzyme (ArM). Such hybrid catalysts display features that are reminiscent of …
artificial metalloenzyme (ArM). Such hybrid catalysts display features that are reminiscent of …
Reversibly photoswitchable protein assemblies with collagen affinity for in vivo photoacoustic imaging of tumors
Recent advancements in photoacoustic (PA) imaging have leveraged reversibly
photoswitchable chromophores, known for their dual absorbance states, to enhance …
photoswitchable chromophores, known for their dual absorbance states, to enhance …
Accelerated enzyme engineering by machine-learning guided cell-free expression
GM Landwehr, JW Bogart, C Magalhaes… - Nature …, 2025 - nature.com
Enzyme engineering is limited by the challenge of rapidly generating and using large
datasets of sequence-function relationships for predictive design. To address this challenge …
datasets of sequence-function relationships for predictive design. To address this challenge …