Directed evolution: methodologies and applications

Y Wang, P Xue, M Cao, T Yu, ST Lane… - Chemical reviews, 2021 - ACS Publications
Directed evolution aims to expedite the natural evolution process of biological molecules
and systems in a test tube through iterative rounds of gene diversifications and library …

Machine-learning-guided directed evolution for protein engineering

KK Yang, Z Wu, FH Arnold - Nature methods, 2019 - nature.com
Protein engineering through machine-learning-guided directed evolution enables the
optimization of protein functions. Machine-learning approaches predict how sequence maps …

The crucial role of methodology development in directed evolution of selective enzymes

G Qu, A Li, CG Acevedo‐Rocha, Z Sun… - Angewandte Chemie …, 2020 - Wiley Online Library
Directed evolution of stereo‐, regio‐, and chemoselective enzymes constitutes a unique way
to generate biocatalysts for synthetically interesting transformations in organic chemistry and …

Learned protein embeddings for machine learning

KK Yang, Z Wu, CN Bedbrook, FH Arnold - Bioinformatics, 2018 - academic.oup.com
Motivation Machine-learning models trained on protein sequences and their measured
functions can infer biological properties of unseen sequences without requiring an …

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 …

Learning epistasis and residue coevolution patterns: Current trends and future perspectives for advancing enzyme engineering

M Wittmund, F Cadet, MD Davari - ACS catalysis, 2022 - ACS Publications
Engineering proteins and enzymes with the desired functionality has broad applications in
molecular biology, biotechnology, biomedical sciences, health, and medicine. The vastness …

Biosystems design by machine learning

MJ Volk, I Lourentzou, S Mishra, LT Vo… - ACS synthetic …, 2020 - ACS Publications
Biosystems such as enzymes, pathways, and whole cells have been increasingly explored
for biotechnological applications. However, the intricate connectivity and resulting …

Computational enzyme redesign: large jumps in function

Y Cui, J Sun, B Wu - Trends in Chemistry, 2022 - cell.com
Rising demands for enzymes in biotechnological applications have fueled efforts to tailor
their properties towards desired functions, such as activity, selectivity, and stability …

[PDF][PDF] 蛋白质工程: 从定向进化到计算设计

曲戈, 朱彤, 蒋迎迎, 吴边, 孙周通 - 生物工程学报, 2019 - researchgate.net
定向进化通过建立突变体文库与高通量筛选方法, 快速提升蛋白的特定性质,
是目前蛋白质工程最为常用的蛋白质设计改造策略. 近十年随着计算机运算能力大幅提升以及 …

In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning

M Vasina, D Kovar, J Damborsky, Y Ding, T Yang… - Biotechnology …, 2023 - Elsevier
Nowadays, the vastly increasing demand for novel biotechnological products is supported
by the continuous development of biocatalytic applications that provide sustainable green …