Hi! My name is Xinyue Ma (马欣悦). I am currently a third-year Ph.D student in Computer Science and Technology at ShanghaiTech University, supervised by Prof. Fang Bai. I received my bachelor's degree in Biomedical Engineering from ShanghaiTech University in 2022.

My research interests focus on Artificial Intelligence-Driven Drug Design(AIDD), including:

• AI methods for protein-nucleic acid interactions: the binding site prediction and generation of nucleic acids.
• Protein representation learning, especially geometric representation based on protein structure.

Publications

Discovery of Selective GluN1/GluN3A NMDA Receptor Inhibitors Using Integrated AI and Physics-Based Approaches.
Shiwei Li*, Yue Zeng*, Sanan Wu*, Xinyue Ma*, Chao Xu*, Zongquan L*, Sui Fang, Xueqin Chen, Zhaobing Gao, Fang Bai
Acta Pharmacologica Sinica, 2025 (Accepted)

NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface.
Xinyue Ma, Fenglei Li, Qianyu Chen, Shenghua Gao, Fang Bai
Journal of Chemical Information and Modeling, 2025 Paper

Recent Advances in Molecular Representation Methods and Their Applications in Scaffold Hopping.
Shihang Wang, Ran Zhang, Xiangcheng Li, Fengyu Cai, Xinyue Ma , et al.
npj Drug Discovery, 2025(Accepted)

PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method.
Lin Wang, Fenglei Li, Xinyue Ma, Yong Cang, Fang Bai
Journal of Chemical Information and Modeling, 2022 Paper

DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs.
Fenglei Li, Qiaoyu Hu, Xianglei Zhang, Renhong Sun, Zhuanghua Liu, Sanan Wu, Siyuan Tian, Xinyue Ma, et al.
Nature Communications, 2022 Paper

* indicates equal contributions.

Talks and Posters

• Speaker of Virtual Graduate Students Symposium in Asia-Pacific Region on Computational Chemistry, ACS2025.
• Speaker of National Conference on Bioinformatics and Systems Biology, 2025.
• Outstanding Poster of FoLST2025, ShanghaiTech. See the poster

Awards

• Outstanding Student of ShanghaiTech University, 2022-2023 and 2023-2024.
• Second Prize of the 2023 Shanghai International Computational Biology Innovation Competition.
  

Experience

Teaching Assistant: Biomedical Statistics (Fall 2022, Spring 2023, Fall 2024)