Binding and sensing diverse small molecules using shape-complementary pseudocycles
We describe an approach for designing high-affinity small molecule–binding proteins poised
for downstream sensing. We use deep learning–generated pseudocycles with repeating …
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 …
bioengineering. Recently, deep learning advances have enabled protein structure …
Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model
Dynamic protein structures are crucial for deciphering their diverse biological functions. Two-
dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid …
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 …
ion beam (FIB), which is referred to as serial lift-out. A block of vitreously frozen biological …
Efficient generation of protein pockets with PocketGen
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 …
intelligence-based design of such proteins is challenging due to the complexity of protein …
Generalized protein pocket generation with prior-informed flow matching
Designing ligand-binding proteins, such as enzymes and biosensors, is essential in
bioengineering and protein biology. One critical step in this process involves designing …
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 …
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 …
core of synthetic biological systems. The history of de novo protein has evolved from initial …
Efficient Generation of Protein Pockets with PocketGen
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 …
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 …
however, excels at this property and its community has created a myriad of circuits and …