Scientific discovery in the age of artificial intelligence

H Wang, T Fu, Y Du, W Gao, K Huang, Z Liu… - Nature, 2023 - nature.com
Artificial intelligence (AI) is being increasingly integrated into scientific discovery to augment
and accelerate research, helping scientists to generate hypotheses, design experiments …

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 …

De novo design of protein structure and function with RFdiffusion

JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim… - Nature, 2023 - nature.com
There has been considerable recent progress in designing new proteins using deep-
learning methods,,,,,,,–. Despite this progress, a general deep-learning framework for protein …

De novo design of luciferases using deep learning

AHW Yeh, C Norn, Y Kipnis, D Tischer, SJ Pellock… - Nature, 2023 - nature.com
De novo enzyme design has sought to introduce active sites and substrate-binding pockets
that are predicted to catalyse a reaction of interest into geometrically compatible native …

Evolutionary-scale prediction of atomic-level protein structure with a language model

Z Lin, H Akin, R Rao, B Hie, Z Zhu, W Lu, N Smetanin… - Science, 2023 - science.org
Recent advances in machine learning have leveraged evolutionary information in multiple
sequence alignments to predict protein structure. We demonstrate direct inference of full …

Illuminating protein space with a programmable generative model

JB Ingraham, M Baranov, Z Costello, KW Barber… - Nature, 2023 - nature.com
Three billion years of evolution has produced a tremendous diversity of protein molecules,
but the full potential of proteins is likely to be much greater. Accessing this potential has …

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 …

Robust deep learning–based protein sequence design using ProteinMPNN

J Dauparas, I Anishchenko, N Bennett, H Bai… - Science, 2022 - science.org
Although deep learning has revolutionized protein structure prediction, almost all
experimentally characterized de novo protein designs have been generated using …

Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim… - BioRxiv, 2022 - biorxiv.org
There has been considerable recent progress in designing new proteins using deep
learning methods–. Despite this progress, a general deep learning framework for protein …

Improving protein expression, stability, and function with ProteinMPNN

KH Sumida, R Núñez-Franco, I Kalvet… - Journal of the …, 2024 - ACS Publications
Natural proteins are highly optimized for function but are often difficult to produce at a scale
suitable for biotechnological applications due to poor expression in heterologous systems …