Principal investigator
Name:
Fang BaiAssociate Professor , PhD, Associate Professor
Position:
Affiliation:
School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies
Honor:
Education Background:
- 2004/09-2009/07, Dalian University of Technology, BE; BA
- 2009/09-2014/05, Dalian University of Technology, Ph.D
Working Experience:
- 2014/08-2019/05, Rice University, Postdoctoral Reserach Fellow
- 2019/05-2019/09, UT Health Science Center at Houston, Assistant Professor of Research
- 2019/10-2025/04, ShanghaiTech University, Assistant Professor (TENURE-TRACK)
- 2025/04-present, Shanghaitech University, Associate Professor(TENURED)
Group Introduction
Research Area:
Drug Design and Developmen
Research Interests:
Our research group is dedicated to the prediction and modulation of protein–protein interactions (PPIs), one of the most challenging classes of undruggable therapeutic targets. We develop computational theories, algorithms, and enabling technologies for innovative drug discovery. To address the dual challenges of high-dimensional complexity and limited data availability in drug design, we establish a collaborative paradigm that integrates physics-based modeling with artificial intelligence-driven approaches, advancing the rational design and discovery of novel therapeutic molecules. Focusing on the entire drug discovery pipeline, we have established a three-tier computational framework for rational drug design and continuously expand its capabilities through methodological and algorithmic innovations: (1) elucidation of protein structural dynamics and functional mechanisms to reveal the conformational landscapes and regulatory principles of biomacromolecules; (2) prediction of protein–protein interactions and precise identification of druggable sites to characterize interaction networks and discover actionable therapeutic targets; and (3) intelligent design of multimodal therapeutic molecules, including occupancy-driven small-molecule modulators and event-driven protein degraders, enabling the rational design and optimization of next-generation therapeutics. Building upon this framework, our research focuses on the development of innovative therapeutics for cancer, metabolic disorders, and broad-spectrum antiviral applications. By integrating artificial intelligence, computational biology, and medicinal chemistry, we aim to provide fundamental theories, advanced computational methodologies, and enabling technologies for the precise modulation of challenging therapeutic targets and the discovery of potential new drugs.
Website of the research group:https://bailab-shanghaitech.siais.shanghaitech.edu.cn/ (new)or https://bailab.siais.shanghaitech.edu.cn/ (old)
Representative Publications (*First Author, # Corresponding Author)
- 1. 胡乔宇*#; 曹宇*; 任鹏璇*; 张向磊; 李风雷; 张学远; 蔡丰彧; 张冉; 周泳锜; 梅良和#; 白芳#.DeepDegradome: A Structure-Aware Deep Learning Framework for PROTAC and Ligand Generation Against Protein Targets.Proceedings of the National Academy of Sciences of the United States of America(PNAS). 17 Mar 2026. 123(11).
- 2. Yongqi Zhou*; Yu Cao; Xinyue Ma; Hao Yang; Siyuan Tian; Chenjia Zhu; Yilin Tang; Ran Zhang; José N. Onuchic#; Fang Bai#.Integrative structural and computational analysis reveals potential design principles for efficient PROTAC degraders.Cell Reports Physical Science. 08 Jul 2026. 7(7).
- 3. Wang, Shihang*; Han, Qilei; Qin, Weichen; Wang, Lin; Yuan, Junhong; Cai, Fengyu; Zhao, Yiqun; Ren, Pengxuan; Zhang, Yunze; Tang, Yilin; Li, Ruifeng; Li, Zongquan; Zhang, Wenchao; Gao, Shenghua#; Bai, Fang#.PhenoModel: A multimodal phenotypic drug design foundation model for discovering novel potential inhibitors of multiple cancer cells.Acta Pharmaceutica Sinica B. Mar 2026. 16(3):1219-1232.
- 4. Wu, Shaoxuan*; Lin, Lin; Hu, Qiaoyu; Yao, Xuebo; Wang, Hongyang; Liu, Shuang; Liu, Qingling; Xi, Yuehui; Lin, Yuzhe; Gong, Jianqiao; Hu, Ruixing; Zhan, Wei; Luo, Yi; He, Guang; Liu, Zhijun; Xiong, Wei; Wang, Qiuju#; Xu, Zhigang#; Bai, Fang#; Lu, Qing#.Mechano-electrical transduction components TMC1-CIB2 undergo a Ca 2+ -induced conformational change linked to hearing loss.DEVELOPMENTAL CELL. 09 Jun 2025. 60(11):1586-1600.e4.
- 5. Wang, Lin*; Wang, Shihang; Yang, Hao; Li, Shiwei; Wang, Xinyu; Zhou, Yongqi; Tian, Siyuan; Liu, Lu; Bai, Fang#.Conformational Space Profiling Enhances Generic Molecular Representation for AI-Powered Ligand-Based Drug Discovery.ADVANCED SCIENCE. Oct 2024. 11(40).
- 6. Yao Hu*; Hao Yang*; Mingwei Li; Zhicheng Zhong; Yongqi Zhou; Fang Bai#; Qian Wang#.Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy.ADVANCED SCIENCE. 26 Nov 2024. 11(44).
- 7. Li, Fenglei*; Hu, Qiaoyu; Zhou, Yongqi; Yang, Hao; Bai, Fang#.DiffPROTACs is a deep learning-based generator for proteolysis targeting chimeras.BRIEFINGS IN BIOINFORMATICS. 05 Aug 2024. 25(5).
- 8. Li, Fenglei*; Hu, Qiaoyu; Zhang, Xianglei; Sun, Renhong; Liu, Zhuanghua; Wu, Sanan; Tian, Siyuan; Ma, Xinyue; Dai, Zhizhuo; Yang, Xiaobao#; Gao, Shenghua#; Bai, Fang#.DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs.NATURE COMMUNICATIONS. 21 Nov 2022. 13(1).
- 9. Wang, Qian*#; Wang, Lin; Zhang, Yumin; Zhang, XiangLei; Zhang, Leike; Shang, Weijuan#; Bai, Fang#.Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications.JOURNAL OF MEDICINAL CHEMISTRY. 24 Feb 2022. 65(4):2827-2835.
- 10. Wang, Lin*; Li, Feng-lei; Ma, Xin-yue; Cang, Yong; Bai, Fang#.PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method.JOURNAL OF CHEMICAL INFORMATION AND MODELING. 12 Dec 2022. 62(23):6160-6171.
- 11. Bai, Fang*; Liu, Kangdong*; Li, Huiliang*; Wang, Jiawei; Zhu, Junsheng; Hao, Pei; Zhu, Lili; Zhang, Shoude; Shan, Lei; Ma, Weiya; Bode, Ann M.; Zhang, Weidong#; Li, Honglin#; Dong, Zigang#.Veratramine modulates AP-1-dependent gene transcription by directly binding to programmable DNA.NUCLEIC ACIDS RESEARCH. 2018. 46(2):546-557.
- 12. Bai, Fang*; Morcos, Faruck; Cheng, Ryan R.; Jiang, Hualiang#; Onuchic, Jose N.#.Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2016. 113(50):8051-8058.
- 13. Bai, Fang*; Morcos, Faruck*; Sohn, Yang-Sung; Darash-Yahana, Merav; Rezende, Celso O.; Lipper, Colin H.; Paddock, Mark L.; Song, Luhua; Luo, Yuting; Holt, Sarah H.; Tamir, Sagi; Theodorakis, Emmanuel A.; Jennings, Patricia A.#; Onuchic, Jose N.#; Mittler, Ron#; Nechushtai, Rachel#.The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2015. 112(12):3698-3703.
- 14. Bai, Fang*; Xu, Yechun; Chen, Jing; Liu, Qiufeng; Gu, Junfeng; Wang, Xicheng; Ma, Jianpeng; Li, Honglin#; Onuchic, Jose N.#; Jiang, Hualiang#.Free energy landscape for the binding process of Huperzine A to acetylcholinesterase.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013. 110(11):4273-4278.
Group Member and Photo
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Name:Xianglei Zhang
Position:Postdoct
Duration:2020.08-present
Email:
-
Name:Pengxuan Ren
Position:Postgraduate Student
Duration:2019.09-present
Email:
-
Name:Lin Wang
Position:Postgraduate Student
Duration:2019.09-present
Email:
-
Name:Ruofan Xiong
Position:Postgraduate Student
Duration:2019.09-present
Email:
-
Name:Shuai Yan
Position:Undergraduate Student
Duration:2020.01-present
Email:
-
Name:Lianghao Zhao
Position:Undergraduate Student
Duration:2020.1-presnet
Email:
-
Name:Wenjing Wu
Position:Undergraduate Student
Duration:2020.02-present
Email:
-
Name:Guo Chen
Position:Undergraduate Student
Duration:2020.2-present
Email:
-
Name:WenXuan Li
Position:Undergraduate Student
Duration:2020.2-present
Email:
-
Name:Xuyang Li
Position:Undergraduate Student
Duration:2020.05-present
Email:
-
Name:Huiqiong Li
Position:Visiting Student
Duration:2019.11-2020.7
Email:
-
Name:Bingqian Li
Position:Visiting Student
Duration:2020.7-2020.9
Email:
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