Binding and sensing diverse small molecules using shape-complementary pseudocycles

L An, M Said, L Tran, S Majumder, I Goreshnik, GR Lee… - Science, 2024 - science.org
We describe an approach for designing high-affinity small molecule–binding proteins poised
for downstream sensing. We use deep learning–generated pseudocycles with repeating …

Protein Design Using Structure-Prediction Networks: AlphaFold and RoseTTAFold as Protein Structure Foundation Models

J Wang, JL Watson, SL Lisanza - Cold Spring Harbor …, 2024 - cshperspectives.cshlp.org
Designing proteins with tailored structures and functions is a long-standing goal in
bioengineering. Recently, deep learning advances have enabled protein structure …

Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model

F Wu, Y Huang, G Yang, S Ye, S Mukamel… - Proceedings of the …, 2024 - pnas.org
Dynamic protein structures are crucial for deciphering their diverse biological functions. Two-
dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid …

[HTML][HTML] Exploring the influence of anionic lipids in the host cell membrane on viral fusion

D Birtles, J Lee - Biochemical Society Transactions, 2024 - portlandpress.com
The image depicts an artistic representation of the lift-out and sectioning step with a focused
ion beam (FIB), which is referred to as serial lift-out. A block of vitreously frozen biological …

Efficient generation of protein pockets with PocketGen

Z Zhang, WX Shen, Q Liu, M Zitnik - Nature Machine Intelligence, 2024 - nature.com
Designing protein-binding proteins is critical for drug discovery. However, artificial-
intelligence-based design of such proteins is challenging due to the complexity of protein …

Generalized protein pocket generation with prior-informed flow matching

Z Zhang, M Zitnik, Q Liu - arxiv preprint arxiv:2409.19520, 2024 - arxiv.org
Designing ligand-binding proteins, such as enzymes and biosensors, is essential in
bioengineering and protein biology. One critical step in this process involves designing …

Confinement and Catalysis within De Novo Designed Peptide Barrels

R Petrenas, OA Hawkins, JF Jones… - Journal of the …, 2025 - ACS Publications
De novo protein design has advanced such that many peptide assemblies and protein
structures can be generated predictably and quickly. The drive now is to bring functions to …

Atomic molecular dynamics simulation advances of de novo-designed proteins

M Wang, A Ma, H Wang, X Lou - Quarterly Reviews of Biophysics, 2024 - cambridge.org
Proteins are vital biological macromolecules that execute biological functions and form the
core of synthetic biological systems. The history of de novo protein has evolved from initial …

Efficient Generation of Protein Pockets with PocketGen

Z Zhang, WX Shen, Q Liu, M Zitnik - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
Designing protein-binding proteins is critical for drug discovery. However, the AI-based
design of such proteins is challenging due to the complexity of ligand-protein interactions …

[HTML][HTML] What can protein circuit design learn from DNA nanotechnology?

D Yu, X Fan, Z Chen - Current Opinion in Biomedical Engineering, 2024 - Elsevier
Protein circuit design is still in its infancy in terms of programmability. DNA nanotechnology,
however, excels at this property and its community has created a myriad of circuits and …