Machine learning for functional protein design

P Notin, N Rollins, Y Gal, C Sander, D Marks - Nature biotechnology, 2024 - nature.com
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and
structure data have radically transformed computational protein design. New methods …

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-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 …

Sourcing thermotolerant poly (ethylene terephthalate) hydrolase scaffolds from natural diversity

E Erickson, JE Gado, L Avilán, F Bratti… - Nature …, 2022 - nature.com
Enzymatic deconstruction of poly (ethylene terephthalate)(PET) is under intense
investigation, given the ability of hydrolase enzymes to depolymerize PET to its constituent …

Embracing data science in catalysis research

M Suvarna, J Pérez-Ramírez - Nature Catalysis, 2024 - nature.com
Accelerating catalyst discovery and development is of paramount importance in addressing
the global energy, sustainability and healthcare demands. The past decade has witnessed …

Machine learning-enabled retrobiosynthesis of molecules

T Yu, AG Boob, MJ Volk, X Liu, H Cui, H Zhao - Nature Catalysis, 2023 - nature.com
Retrobiosynthesis provides an effective and sustainable approach to producing functional
molecules. The past few decades have witnessed a rapid expansion of biosynthetic …

De novo protein design by deep network hallucination

I Anishchenko, SJ Pellock, TM Chidyausiku… - Nature, 2021 - nature.com
There has been considerable recent progress in protein structure prediction using deep
neural networks to predict inter-residue distances from amino acid sequences,–. Here we …

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

A Rives, J Meier, T Sercu, S Goyal, Z Lin, J Liu… - Proceedings of the …, 2021 - pnas.org
In the field of artificial intelligence, a combination of scale in data and model capacity
enabled by unsupervised learning has led to major advances in representation learning and …

Utilizing graph machine learning within drug discovery and development

T Gaudelet, B Day, AR Jamasb, J Soman… - Briefings in …, 2021 - academic.oup.com
Graph machine learning (GML) is receiving growing interest within the pharmaceutical and
biotechnology industries for its ability to model biomolecular structures, the functional …

Transformer protein language models are unsupervised structure learners

R Rao, J Meier, T Sercu, S Ovchinnikov, A Rives - Biorxiv, 2020 - biorxiv.org
Unsupervised contact prediction is central to uncovering physical, structural, and functional
constraints for protein structure determination and design. For decades, the predominant …