Yuqi Shi

This study identifies health-associated gut bacteriocins that target TLR4 to suppress intestinal inflammation in murine models.

MetaReact predicts drug metabolites and enzyme selectivity using a reaction-aware Transformer, outperforming existing methods in accuracy and generalizability.

This study investigates the allosteric effects of the coupling cation in the melibiose transporter MelB by integrating structural, HDX-MS, and simulation data to reveal how cation binding enhances sugar-binding affinity through conformational restraint.

The paper introduces IIBacFinder to identify unmodified class II bacteriocins in the human gut microbiome, showing their widespread distribution and biosynthetic potential.

This study reveals that membrane phosphoinositides allosterically regulate β-arrestin dynamics, enabling engagement with minimally phosphorylated GPCRs.

The paper introduces ConfSeq, a conformation description language for 3D molecular structures, enabling sequence-based modeling and achieving state-of-the-art results in 3D molecular tasks.

This study identifies diverse ribosomally synthesized peptides in the human microbiome and shows some inhibit pathogens and reduce inflammation.

The paper demonstrates how data-independent acquisition methods can automate hydrogen/deuterium exchange mass spectrometry measurements with improved precision and throughput.

This study investigates the structural dynamics of USP30 inhibition by a covalent inhibitor, revealing its binding mechanism and selectivity advantages over non-covalent inhibitors.

This study discovers new Avi(Me)Cys-containing cyclopeptide antibiotics effective against drug-resistant bacteria using genome mining and metabolomics.

This paper presents a fast and accurate method for detecting disulfide bridges in proteins using mass spectrometry with optimized sample preparation and data analysis.

This study determines the structure and dynamics of a Na+-coupled sugar transporter, revealing how mobile barriers regulate substrate binding and release.