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 …

Spike deep mutational scanning helps predict success of SARS-CoV-2 clades

B Dadonaite, J Brown, TE McMahon, AG Farrell… - Nature, 2024 - nature.com
SARS-CoV-2 variants acquire mutations in the spike protein that promote immune evasion
and affect other properties that contribute to viral fitness, such as ACE2 receptor binding and …

Virology—The next fifty years

EC Holmes, F Krammer, FD Goodrum - Cell, 2024 - cell.com
Virology has made enormous advances in the last 50 years but has never faced such
scrutiny as it does today. Herein, we outline some of the major advances made in virology …

Proteinnpt: Improving protein property prediction and design with non-parametric transformers

P Notin, R Weitzman, D Marks… - Advances in Neural …, 2023 - proceedings.neurips.cc
Protein design holds immense potential for optimizing naturally occurring proteins, with
broad applications in drug discovery, material design, and sustainability. However …

Evaluating generalizability of artificial intelligence models for molecular datasets

Y Ektefaie, A Shen, D Bykova, MG Marin… - Nature Machine …, 2024 - nature.com
Deep learning has made rapid advances in modelling molecular sequencing data. Despite
achieving high performance on benchmarks, it remains unclear to what extent deep learning …

International Scientific Report on the Safety of Advanced AI (Interim Report)

Y Bengio, S Mindermann, D Privitera… - arxiv preprint arxiv …, 2024 - arxiv.org
This is the interim publication of the first International Scientific Report on the Safety of
Advanced AI. The report synthesises the scientific understanding of general-purpose AI--AI …

[HTML][HTML] Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades

B Dadonaite, J Brown, TE McMahon, AG Farrell… - biorxiv, 2023 - ncbi.nlm.nih.gov
SARS-CoV-2 variants acquire mutations in spike that promote immune evasion and impact
other properties that contribute to viral fitness such as ACE2 receptor binding and cell entry …

[HTML][HTML] User-friendly and industry-integrated AI for medicinal chemists and pharmaceuticals

O Kapustina, P Burmakina, N Gubina, N Serov… - Artificial Intelligence …, 2024 - Elsevier
Artificial intelligence has brought crucial changes to the whole field of natural sciences.
Myriads of machine learning algorithms have been developed to facilitate the work of …

A unified evolution-driven deep learning framework for virus variation driver prediction

Z Nie, X Liu, J Chen, Z Wang, Y Liu, H Si… - Nature Machine …, 2025 - nature.com
The increasing frequency of emerging viral infections necessitates a rapid human response,
highlighting the cost-effectiveness of computational methods. However, existing …

Exploring the ability of the MD+ FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data

LA Chi, JE Barnes, JS Patel, FM Ytreberg - Scientific Reports, 2024 - nature.com
Antibody escape mutations pose a significant challenge to the effectiveness of vaccines and
antibody-based therapies. The ability to predict these escape mutations with computer …