Theoretical and computational simulation on the mechanism of protein folding and allostery, the conformation ensemble and dynamics of intrinsically disordered proteins, as well as the mechanism of protein phase separation; data mining using mechine learning.

   

2005-2007 Postdoctoral Fellow, College of Chemistry and Molecular Engineering, Center for Theoretical Biology, Peking University 

2008-2011 Postdoctoral Fellow, Departments of Biochemistry, University of Toronto 

2011.6-present Associate Professor, Professor, College of Life Sciences, University of Chinese Academy of Sciences

"Single-molecule techniques in biology", 2012-2015

"Computational Biology", 2012-2015

   

Selected Publications：

1. Shaofeng Liao, Yujun Zhang, Yifei Qi^*, Zhuqing Zhang^*. Evaluation of sequences-based predictors for phase separating protein. Brief Bioinform. 2023: 24(4):bbad213.

2. Xiaoquan Chu^†, Tanlin Sun^†, Qian Li, Youjun Xu, Zhuqing Zhang^*, Luhua Lai^*, Jianfeng Pei^*. Prediction of liquid-liquid phase separating proteins using machine learning. BMC Bioinformatics. 2022:23(1):72 [Highly Cited Papers, 2023]

3. Xi Wang^†, Xiang Zhou^†, Qinglin Yan^†, Shaofeng Liao, Wenqin Tang, Peiyu Xu, Yangzhenyu Gao, Qian Li, Zhihui Dou, Weishan Yang, Beifang Huang, Jinhong Li, Zhuqing Zhang^*. LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro. Bioinformatics. 2022:38(7):2010-2014 (^†equal contribution)

4. Qian Li^†, Xiaojun Peng^†, Yuanqing Li, Wenqin Tang, Jia'an Zhu, Jing Huang, Yifei Qi and Zhuqing Zhang^*. LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro. Nucleic Acids Res. 2020:48:D320-327 (^†equal contribution) [ F1000Prime: https://f1000.com/prime/736585742]

5. Likun Zhao, Luhua Lai^*, Zhuqing Zhang^*. How calcium ion binding induces the conformational transition of the calmodulin N-terminal domain-an atomic level characterization. Phys Chem Chem Phys. 2019,21;19795-19804. [2019 PCCP HOT ARTICLE]

6.Yanhua Ouyang, Likun Zhao, Zhuqing Zhang^*. Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields. Phys Chem Chem Phys. 2018,20:8676-8684.

7. Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan^*, Zhuqing Zhang^*. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding. Phys Chem Chem Phys. 2017,19:13629-13639. [2017 PCCP HOT ARTICLE]

8. Zhuqing Zhang^*, Yanhua Ouyang, Tao Chen. Influences of heterogeneous native contact energy and many-body interactions on the prediction of protein folding mechanisms. Phys Chem Chem Phys. 2016,18:31304-31311

9. Zhuqing Zhang, and Hue Sun Chan^*. Transition paths, diffusive processes, and preequilibria of protein folding.  Proc Natl Acad Sci U S A. 2012,109:20919-20924

10. Hue Sun Chan^*, Zhuqing Zhang, Stefan Wallin and Zhirong Liu. Native Topology, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models. Annu Rew Phys Chem. 2011,62:301-332

11. Zhuqing Zhang, and Hue Sun Chan^*. Competition between Native Topology and Nonnative Interactions in Simple and Complex Folding Kinetics of Natural and Designed Proteins. Proc Natl Acad Sci U S A. 2010,107:2920-2925

12.  Zhuqing Zhang, Hao Chen, Luhua Lai^*. Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential. Bioinformatics. 2007,23:2218-2225

13. Zhuqing Zhang, Hao Chen, Hongjun Bai, Luhua Lai^*. Molecular dynamics simulations on the oligomer formation process of the GNNQQNY peptide from yeast prion protein Sup35. Biophys J. 2007,93;1484-1492