Opportunities and challenges in design and optimization of protein function

D Listov, CA Goverde, BE Correia… - … Reviews Molecular Cell …, 2024‏ - nature.com
The field of protein design has made remarkable progress over the past decade. Historically,
the low reliability of purely structure-based design methods limited their application, but …

[HTML][HTML] De novo protein design—From new structures to programmable functions

T Kortemme - Cell, 2024‏ - cell.com
Methods from artificial intelligence (AI) trained on large datasets of sequences and
structures can now" write" proteins with new shapes and molecular functions de novo …

Mega-scale experimental analysis of protein folding stability in biology and design

K Tsuboyama, J Dauparas, J Chen, E Laine… - Nature, 2023‏ - nature.com
Advances in DNA sequencing and machine learning are providing insights into protein
sequences and structures on an enormous scale. However, the energetics driving folding …

Learning inverse folding from millions of predicted structures

C Hsu, R Verkuil, J Liu, Z Lin, B Hie… - International …, 2022‏ - proceedings.mlr.press
We consider the problem of predicting a protein sequence from its backbone atom
coordinates. Machine learning approaches to this problem to date have been limited by the …

Design of protein-binding proteins from the target structure alone

L Cao, B Coventry, I Goreshnik, B Huang, W Sheffler… - Nature, 2022‏ - nature.com
The design of proteins that bind to a specific site on the surface of a target protein using no
information other than the three-dimensional structure of the target remains a challenge …

De novo design of high-affinity binders of bioactive helical peptides

S Vázquez Torres, PJY Leung, P Venkatesh, ID Lutz… - Nature, 2024‏ - nature.com
Many peptide hormones form an α-helix on binding their receptors,,–, and sensitive methods
for their detection could contribute to better clinical management of disease. De novo protein …

De novo design of protein interactions with learned surface fingerprints

P Gainza, S Wehrle, A Van Hall-Beauvais, A Marchand… - Nature, 2023‏ - nature.com
Physical interactions between proteins are essential for most biological processes
governing life. However, the molecular determinants of such interactions have been …

Improving de novo protein binder design with deep learning

NR Bennett, B Coventry, I Goreshnik, B Huang… - Nature …, 2023‏ - nature.com
Recently it has become possible to de novo design high affinity protein binding proteins from
target structural information alone. There is, however, considerable room for improvement as …

ProteinBERT: a universal deep-learning model of protein sequence and function

N Brandes, D Ofer, Y Peleg, N Rappoport… - …, 2022‏ - academic.oup.com
Self-supervised deep language modeling has shown unprecedented success across natural
language tasks, and has recently been repurposed to biological sequences. However …

Learning protein fitness models from evolutionary and assay-labeled data

C Hsu, H Nisonoff, C Fannjiang, J Listgarten - Nature biotechnology, 2022‏ - nature.com
Abstract Machine learning-based models of protein fitness typically learn from either
unlabeled, evolutionarily related sequences or variant sequences with experimentally …