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 …

Machine learning and deep learning in synthetic biology: Key architectures, applications, and challenges

MK Goshisht - ACS omega, 2024 - ACS Publications
Machine learning (ML), particularly deep learning (DL), has made rapid and substantial
progress in synthetic biology in recent years. Biotechnological applications of biosystems …

Predicting a protein's stability under a million mutations

J Ouyang-Zhang, D Diaz, A Klivans… - Advances in Neural …, 2024 - proceedings.neurips.cc
Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary
pressure of all extant proteins makes identifying the scarce number of mutations that will …

Data‐Driven Protein Engineering for Improving Catalytic Activity and Selectivity

YF Ao, M Dörr, MJ Menke, S Born, E Heuson… - …, 2024 - Wiley Online Library
Protein engineering is essential for altering the substrate scope, catalytic activity and
selectivity of enzymes for applications in biocatalysis. However, traditional approaches, such …

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 …

Advancing microbial production through artificial intelligence-aided biology

X Gong, J Zhang, Q Gan, Y Teng, J Hou, Y Lyu… - Biotechnology …, 2024 - Elsevier
Microbial cell factories (MCFs) have been leveraged to construct sustainable platforms for
value-added compound production. To optimize metabolism and reach optimal productivity …

Computational and Machine Learning Methods for CO2 Capture Using Metal–Organic Frameworks

H Mashhadimoslem, MA Abdol, P Karimi… - ACS …, 2024 - ACS Publications
Machine learning (ML) using data sets of atomic and molecular force fields (FFs) has made
significant progress and provided benefits in the fields of chemistry and material science …

Simplification of Corticosteroids Biosynthetic Pathway by Engineering P450BM3

Q Chen, Z Chao, K Wang, X Wang, H Meng, X Liu… - ACS …, 2024 - ACS Publications
Synthesis of corticosteroids, particularly hydrocortisone, is challenging owing to the complex
network requiring pairing of cytochrome P450s with cytochrome P450 reductase (CPR) for …

FAIR Data and Software: Improving Efficiency and Quality of Biocatalytic Science

J Pleiss - ACS Catalysis, 2024 - ACS Publications
Biocatalysis is entering a promising era as a data-driven science. High-throughput
experimentation generates a rapidly increasing stream of biocatalytic data, which is the raw …

Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort

AM Illig, NE Siedhoff, MD Davari… - Journal of Chemical …, 2024 - ACS Publications
Protein engineering through directed evolution and (semi) rational approaches is routinely
applied to optimize protein properties for a broad range of applications in industry and …