3 papers
physics.chem-ph2025
BioMD: All-atom Generative Model for Biomolecular Dynamics Simulation
Bin Feng, Jiying Zhang, Xinni Zhang +2
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their uti…
physics.comp-ph2025
A Novel 4-D Dataset Paradigm for Studying Complete Ligand-Protein Dissociation Dynamics
Maodong Li, Jiying Zhang, Zhe Wang +7
The kinetics and dynamics of drug-protein binding and dissociation are crucial to understanding drug absorption and metabolism. Despite advances in artificial intelligence (AI) too…
cs.LG2024
Efficient Antibody Structure Refinement Using Energy-Guided SE(3) Flow Matching
Jiying Zhang, Zijing Liu, Shengyuan Bai +3
Antibodies are proteins produced by the immune system that recognize and bind to specific antigens, and their 3D structures are crucial for understanding their binding mechanism an…