From nature to industry: Harnessing enzymes for biocatalysis

R Buller, S Lutz, RJ Kazlauskas, R Snajdrova… - Science, 2023 - science.org
Biocatalysis harnesses enzymes to make valuable products. This green technology is used
in countless applications from bench scale to industrial production and allows practitioners …

Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

Functional annotation of enzyme-encoding genes using deep learning with transformer layers

GB Kim, JY Kim, JA Lee, CJ Norsigian… - Nature …, 2023 - nature.com
Functional annotation of open reading frames in microbial genomes remains substantially
incomplete. Enzymes constitute the most prevalent functional gene class in microbial …

Artificial intelligence for science in quantum, atomistic, and continuum systems

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y Xie… - arXiv preprint arXiv …, 2023 - arxiv.org
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural
sciences. Today, AI has started to advance natural sciences by improving, accelerating, and …

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

J Zhang, F Li, D Liu, Q Liu, H Song - Chemical Society Reviews, 2024 - pubs.rsc.org
The excessive consumption of fossil fuels causes massive emission of CO2, leading to
climate deterioration and environmental pollution. The development of substitutes and …

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 …

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 …

New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

KW Chen, TY Sun, YD Wu - Chemical Reviews, 2023 - ACS Publications
A survey of protein databases indicates that the majority of enzymes exist in oligomeric
forms, with about half of those found in the UniProt database being homodimeric …

Accelerating biocatalysis discovery with machine learning: a paradigm shift in enzyme engineering, discovery, and design

B Markus, K Andreas, K Arkadij, L Stefan, O Gustav… - ACS …, 2023 - ACS Publications
Emerging computational tools promise to revolutionize protein engineering for biocatalytic
applications and accelerate the development timelines previously needed to optimize an …

Discovering functionally important sites in proteins

M Cagiada, S Bottaro, S Lindemose… - Nature …, 2023 - nature.com
Proteins play important roles in biology, biotechnology and pharmacology, and missense
variants are a common cause of disease. Discovering functionally important sites in proteins …