12 papers
Enhancing Spatial Reasoning in Large Language Models for Metal-Organic Frameworks Structure Prediction
Mianzhi Pan, JianFei Li, Peishuo Liu +5
Metal-organic frameworks (MOFs) are porous crystalline materials with broad applications such as carbon capture and drug delivery, yet accurately predicting their 3D structures rem…
FLEX: Continuous Agent Evolution via Forward Learning from Experience
Zhicheng Cai, Xinyuan Guo, Yu Pei +7
Autonomous agents driven by Large Language Models (LLMs) have revolutionized reasoning and problem-solving but remain static after training, unable to grow with experience as intel…
Learning Protein-Ligand Binding in Hyperbolic Space
Jianhui Wang, Wenyu Zhu, Bowen Gao +4
Protein-ligand binding prediction is central to virtual screening and affinity ranking, two fundamental tasks in drug discovery. While recent retrieval-based methods embed ligands…
SDrug: Bridging Protein Sequence and 3D Structure in Contrastive Representation Learning for Virtual Screening
Bowei He, Bowen Gao, Yankai Chen +5
Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learnin…
AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation
Wenyu Zhu, Jianhui Wang, Bowen Gao +5
Virtual screening (VS) is a critical component of modern drug discovery, yet most existing methods--whether physics-based or deep learning-based--are developed around holo protein…
Coder as Editor: Code-driven Interpretable Molecular Optimization
Wenyu Zhu, Chengzhu Li, Xiaohe Tian +7
Molecular optimization is a central task in drug discovery that requires precise structural reasoning and domain knowledge. While large language models (LLMs) have shown promise in…