Opportunities and challenges for machine learning-assisted enzyme engineering

J Yang, FZ Li, FH Arnold - ACS Central Science, 2024 - ACS Publications
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 …

Automated in vivo enzyme engineering accelerates biocatalyst optimization

E Orsi, L Schada von Borzyskowski, S Noack… - Nature …, 2024 - nature.com
Achieving cost-competitive bio-based processes requires development of stable and
selective biocatalysts. Their realization through in vitro enzyme characterization and …

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh… - Science, 2024 - science.org
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 …

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 …

Strategies for designing biocatalysts with new functions

EL Bell, AE Hutton, AJ Burke, A O'Connell… - Chemical Society …, 2024 - pubs.rsc.org
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 …

Protein design using structure-prediction networks: AlphaFold and RoseTTAFold as protein structure foundation models

J Wang, JL Watson, SL Lisanza - Cold Spring Harbor …, 2024 - cshperspectives.cshlp.org
Designing proteins with tailored structures and functions is a long-standing goal in
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 …

Recent advances in the design and optimization of artificial metalloenzymes

I Morita, TR Ward - Current Opinion in Chemical Biology, 2024 - Elsevier
Embedding a catalytically competent transition metal into a protein scaffold affords an
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

S Chen, K Li, X Chen, S Lei, J Lin, P Huang - Science Advances, 2024 - science.org
Recent advancements in photoacoustic (PA) imaging have leveraged reversibly
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 …