Publications

You can also find my articles on my Google Scholar profile.

’#’ as (co-)first authorship, ‘*’ as corresponding author.

Content

📋 Chemical Language Models

Token-Mol 1.0: Tokenized drug design with large language model

Jike Wang^#, Rui Qin^#, Mingyang Wang^#, Meijing Fang, Yangyang Zhang, Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun Jiang, Xujun Zhang, Huifeng Zhao, Jingxuan Ge, Zhourui Wu, Yu Kang*, Chang-Yu Hsieh*, Tingjun Hou*
Nature Communications, 16: 4416. 2025
Paper | arXiv | code

3D Molecular Pocket-based Generation with Token-only Large Language Model

Jike Wang^#, Hao Luo^#, Rui Qin^#, Mingyang Wang, Meijing Fang, Odin Zhang, Qiaolin Gou, Qun Su, Chao Shen, Ziyi You, Xiaozhe Wan, Liwei Liu*, Chang-Yu Hsieh*, Tingjun Hou*, Yu Kang*
Chemical Science, 16, 637–648. 2025
Paper | ChemRxiv | code

📋 Generative Models in Drug Design

Deep Learning-based Design and Screening of Benzimidazole-pyrazine Derivatives as Adenosine A_2B Receptor Antagonists

Rui Qin^#, Hao Zhang, Weifeng Huang, Zhenglin Shao, Jinping Lei*
Journal of Biomolecular Structure & Dynamics. 43(7), 3225–3241. 2023
Paper | code

📋 Virtual Screening or Molecular Dynamics

Discovery of Novel Benzo[4,5]imidazo[1,2-a]pyrazin-1-amine-3-amide-one Derivatives as Anticancer Human A_2A Adenosine Receptor Antagonists

Shuhao Liu^#, Wen Ding^#, Weifeng Huang^#, Zhijing Zhang, Yinfeng Guo, Qiyi Zhang, Linna Wu, Yukai Li, Rui Qin, Jiahao Li, Taoda Shi*, Xiaolei Zhang*, Jinping Lei*, Wenhao Hu*
Journal of Medicinal Chemistry, 65(13), 8933–8947. 2022
Paper