Structure (London, England : 1993)
Feb 12, 2025
In cryo-electron microscopy, accurate particle localization and classification are imperative. Recent deep learning solutions, though successful, require extensive training datasets. The protracted generation time of physics-based models, often emplo...
Structure (London, England : 1993)
Nov 1, 2024
The identification of protein binding residues is essential for understanding their functions in vivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue...
Structure (London, England : 1993)
Oct 25, 2024
The high binding affinity of antibodies toward their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as research and therapeutic tools. Here, we propose ANTIPASTI, a convolutional neural network mod...
Structure (London, England : 1993)
Mar 20, 2024
Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational approaches to design a suite of tetrahedrally symmetric, se...
Structure (London, England : 1993)
Mar 19, 2024
Protein missense mutations and resulting protein stability changes are important causes for many human genetic diseases. However, the accurate prediction of stability changes due to mutations remains a challenging problem. To address this problem, we...
Structure (London, England : 1993)
Mar 5, 2024
Identifying binding compounds against a target protein is crucial for large-scale virtual screening in drug development. Recently, network-based methods have been developed for compound-protein interaction (CPI) prediction. However, they are difficul...
Structure (London, England : 1993)
Feb 6, 2024
The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones ...
Structure (London, England : 1993)
Oct 16, 2023
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence (AI) have a burgeoning synergy. Deep learning-based structural predictors have forever changed structural biology, yet these tools currently face limitations in ac...
Structure (London, England : 1993)
May 29, 2023
Building accurate protein models into moderate resolution (3-5 Å) cryoelectron microscopy (cryo-EM) maps is challenging and error prone. We have developed MEDIC (Model Error Detection in Cryo-EM), a robust statistical model that identifies local back...
Structure (London, England : 1993)
Jan 31, 2022
Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are...