Tong Wang Ph.D.
Assistant Professor
2010-2014 B.S., School of Life Sciences, Shandong University
2014-2019 Ph.D., School of Life Sciences, Tsinghua University
2019-2025 Senior Researcher, Microsoft Research
2025-present Assistant Professor, School of Life Sciences, Tsinghua University
2025-present PI, Tsinghua-Peking Center for Life Sciences and Beijing Frontier Research Center for Biological Structure
Research interest
Our lab is dedicated to pushing the frontier of “AI” + “biological molecular structures” studies in methodology design and real-world applications. By designing cutting-edge deep learning techniques, we do molecular structure representation learning, molecular property and interaction predictions, molecular dynamics simulation and protein design, with the aim of revealing the dynamic mechanism of bioactivities and facilitating drug discovery. The specific research directions are:
1) AI driven biomolecular dynamics simulation and its applications in biomechanism detection. (Wang et al, Nature, 2024; Lan et al, Cell Res, 2022; Zhang et al, Cell Res, 2022)
2) Graph neural network, geometric deep learning and machine learning force field. (Wang et al, Nat Commun, 2024; Li et al, ICLR, 2024; Wang et al, NIPS, 2023)
3) AI aided drug discovery and molecular property prediction. (Li et al, Brief Bioinform, 2023; Liu et al, Brief Bioinform, 2023; Wang et al, Nat Mach Intell, 2019)
Selected publications
1. Wang, T.#*; He, X.#; Li, M.#; Li, Y.#; Bi, R.; Wang, Y.; Cheng, C.; Shen, X.; Meng, J.; Zhang, H.; Liu, H.; Wang, Z.; Li, S.; Shao, B.*; Liu, T. “Ab initio characterization of protein molecular dynamics with AI2BMD”. Nature, 2024, 635, 1019-1027.
2. Wang, Y.#; Wang, T.#*, Li, S.#; He, X.; Li, M.; Wang, Z.; Zheng, N.; Shao, B.; Liu, T. “Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing”. Nat Commun, 2024, 15 (1), 313. Editors’ Highlights.
3. Li, Y.#; Wang, Y.#; Huang, L.*; Yang, H.; Wei, X.; Zhang, J.*; Wang, T.*; Wang, Z.; Shao, B.; Liu, T. “Long-short-range message-passing: A physics-informed framework to capture non-local interaction for scalable molecular dynamics simulation”. Proc Int Conf Learn Represent (ICLR), 2024.
4. Wang, T.#*; He, X.#; Li, M.#; Shao, B.*; Liu, T. “AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics”. Sci Data, 2023, 10 (1), 549.
5. Wang, Y.#; Li, S.#; Wang, T.*; Shao, B.; Zheng, N.; Liu. T. “Geometric transformer with interatomic positional encoding”. Proc Adv Neural Inf Process Syst (NeurIPS), 2023, 36, 55981-55994.
6. Wang, Z.#; Wu, H.#; Sun, L.; He, X.; Liu, Z.; Shao, B.; Wang, T.*; Liu, T. “Improving machine learning force fields for molecular dynamics simulations with fine-grained force metrics”. J Chem Phys, 2023, 159(3). Cover story.
7. Li, Z.#; Zhu, S.#; Shao, B.*; Zeng, X.*; Wang, T.*; Liu, T. “DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning”. Brief Bioinform, 2023, 24 (1), bbac597.
8. Lan, J.#; He, X.#; Ren, Y.#; Wang, Z.#; Zhou, H.; Fan, S.; Zhu, C.; Liu, D.; Shao, B.; Liu, T.; Wang, Q.; Zhang, L.*; Ge, J.*; Wang, T.*; Wang, X.*. “Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction”. Cell Res, 2022, 32, 593-595.
9. Zhang, S.#; Liang, Q.#; He, X.; Zhao, C.; Ren, W.; Yang, Z.; Wang, Z.; Ding, Q.; Deng, H.; Wang, T.*; Zhang, L.*; Wang, X.*. “Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2”. Cell Res, 2022, 32, 315-318.
10. Gong, S.#; He, X.#; Meng, Q.; Ma, Z.; Shao, B.*; Wang, T.*; Liu, T. “Stochastic Lag Time Parameterization for Markov State Models of Protein Dynamics” J Phys Chem B, 2022, 126 (46), 9465-9475. Cover story.
11. Liu, S.#; Wang, Y.#; Deng, Y.; He, L.; Shao, B.; Yin, J.; Zheng, N.; Liu, T.; Wang, T*. “Improved drug–target interaction prediction with intermolecular graph transformer”. Brief Bioinform, 2022, 23 (5), bbac162.
12. Li, Y.#; Wang, T.#*; Zhang, J.#; Shao, B.; Gong, H.*; Liu, T. “Exploring the Regulatory Function of the N‐terminal Domain of SARS‐CoV‐2 Spike Protein through Molecular Dynamics Simulation”. Adv Theor Simul, 2021, 4 (10), 2100152. Cover story & “Top Downloaded Article” Award.
13. Wang, T.; Qiao, Y.; Ding, W.; Mao, W.; Zhou, Y.*; Gong, H.*. “Improved fragment sampling for ab initio protein structure prediction using deep neural networks”. Nat Mach Intell, 2019, 1 (8), 347-355. Highlighted: Nat Mach Intell, 2019, 1 (8), 336-337.
#: Co-first author; *: Corresponding author
Awards
Top 10 Advances in Chinese Bioinformatics in 2024 (2024)
Champion in The First Global AI Drug Development Competition (2023)
Contact information
E-mail：tongwang@mail.tsinghua.edu.cn
Address: A216-1, Bio-Medical Building, School of Life Sciences, Tsinghua University, Beijing, 100084, China
