8 papers
BioMiner: A Multi-modal System for Automated Mining of Protein-Ligand Bioactivity Data from Literature
Jiaxian Yan, Jintao Zhu, Yuhang Yang +8
Protein-ligand bioactivity data published in the literature are essential for drug discovery, yet manual curation struggles to keep pace with rapidly growing literature. Automated…
A Biosecurity Agent for Lifecycle LLM Biosecurity Alignment
Meiyin Meng, Zaixi Zhang
Large language models (LLMs) are increasingly integrated into biomedical research workflows--from literature triage and hypothesis generation to experimental design--yet this expan…
GraphPrompter: Multi-stage Adaptive Prompt Optimization for Graph In-Context Learning
Rui Lv, Zaixi Zhang, Kai Zhang +6
Graph In-Context Learning, with the ability to adapt pre-trained graph models to novel and diverse downstream graphs without updating any parameters, has gained much attention in t…
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…