[HTML][HTML] Learning the protein language: Evolution, structure, and function

T Bepler, B Berger - Cell systems, 2021 - cell.com
Language models have recently emerged as a powerful machine-learning approach for
distilling information from massive protein sequence databases. From readily available …

MSA transformer

RM Rao, J Liu, R Verkuil, J Meier… - International …, 2021 - proceedings.mlr.press
Unsupervised protein language models trained across millions of diverse sequences learn
structure and function of proteins. Protein language models studied to date have been …

Learning functional properties of proteins with language models

S Unsal, H Atas, M Albayrak, K Turhan… - Nature Machine …, 2022 - nature.com
Data-centric approaches have been used to develop predictive methods for elucidating
uncharacterized properties of proteins; however, studies indicate that these methods should …

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

A Rives, J Meier, T Sercu, S Goyal… - Proceedings of the …, 2021 - National Acad Sciences
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 …

Large-scale chemical language representations capture molecular structure and properties

J Ross, B Belgodere, V Chenthamarakshan… - Nature Machine …, 2022 - nature.com
Abstract Models based on machine learning can enable accurate and fast molecular
property predictions, which is of interest in drug discovery and material design. Various …

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 …

Pre-trained language models in biomedical domain: A systematic survey

B Wang, Q Xie, J Pei, Z Chen, P Tiwari, Z Li… - ACM Computing …, 2023 - dl.acm.org
Pre-trained language models (PLMs) have been the de facto paradigm for most natural
language processing tasks. This also benefits the biomedical domain: researchers from …

Graph denoising diffusion for inverse protein folding

K Yi, B Zhou, Y Shen, P Liò… - Advances in Neural …, 2024 - proceedings.neurips.cc
Inverse protein folding is challenging due to its inherent one-to-many mapping
characteristic, where numerous possible amino acid sequences can fold into a single …

[HTML][HTML] Antibody structure prediction using interpretable deep learning

JA Ruffolo, J Sulam, JJ Gray - Patterns, 2022 - cell.com
Therapeutic antibodies make up a rapidly growing segment of the biologics market.
However, rational design of antibodies is hindered by reliance on experimental methods for …

[HTML][HTML] Transformer-based deep learning for predicting protein properties in the life sciences

A Chandra, L Tünnermann, T Löfstedt, R Gratz - Elife, 2023 - elifesciences.org
Recent developments in deep learning, coupled with an increasing number of sequenced
proteins, have led to a breakthrough in life science applications, in particular in protein …