4 papers
Geometric Deep Learning for Structure-Based Drug Design: A Survey
Zaixi Zhang, Jiaxian Yan, Yining Huang +4
Structure-based drug design (SBDD) leverages the three-dimensional geometry of proteins to identify potential drug candidates. Traditional approaches, rooted in physicochemical mod…
DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking
Jiaxian Yan, Zaixi Zhang, Jintao Zhu +3
Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in…
FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling
Zaixi Zhang, Mengdi Wang, Qi Liu
Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically…
Generalized Protein Pocket Generation with Prior-Informed Flow Matching
Zaixi Zhang, Marinka Zitnik, Qi Liu
Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein…