8 citations · 39 across the 26 of their papers we have counts for
9 papers · 1 filter
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…
Coder as Editor: Code-driven Interpretable Molecular Editing
Wenyu Zhu, Chengzhu Li, Xiaohe Tian +8
Molecular design is a central task in drug discovery that requires precise structural reasoning and domain knowledge. While large language models (LLMs) have shown promise in gener…
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…
Revisiting Sampling Strategies for Molecular Generation
Yuyan Ni, Shikun Feng, Wei-Ying Ma +2
Sampling strategies in diffusion models are critical to molecular generation yet remain relatively underexplored. In this work, we investigate a broad spectrum of sampling methods…
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…
Manipulating 3D Molecules in a Fixed-Dimensional E(3)-Equivariant Latent Space
Zitao Chen, Yinjun Jia, Zitong Tian +2
Medicinal chemists often optimize drugs considering their 3D structures and designing structurally distinct molecules that retain key features, such as shapes, pharmacophores, or c…
PharmAgents: Building a Virtual Pharma with Large Language Model Agents
Bowen Gao, Yanwen Huang, Yiqiao Liu +4
The discovery of novel small molecule drugs remains a critical scientific challenge with far-reaching implications for treating diseases and advancing human health. Traditional dru…
Pushing the boundaries of Structure-Based Drug Design through Collaboration with Large Language Models
Bowen Gao, Yanwen Huang, Yiqiao Liu +4
Structure-Based Drug Design (SBDD) has revolutionized drug discovery by enabling the rational design of molecules for specific protein targets. Despite significant advancements in…
Straight-Line Diffusion Model for Efficient 3D Molecular Generation
Yuyan Ni, Shikun Feng, Haohan Chi +5
Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a…