部分论文列表：

1.   Z Zhang, Y Zhang, W Ren*, W Zhang, W Li*, W Wang*

Allosteric Regulation of Enzymatic Catalysis through Mechanical Force

J. Chem. Theory Comput., 2025, doi.org/10.1021/acs.jctc.5c00250

2.   L Chen^#, X Zhou^#, Y Huang^#, X Wang, X Gao, Y Cao, W Li*, Y Zhou*

Chirality Interplay of Peptide and Saccharide on Glycopeptide Self-Assembly

Nano Lett. 2025, 25, 4, 1558–1566

3.   C Li^#, Y Bian^#, Y Tang^#, L Meng, P Yin, Y Hong, J Cheng, Y Li, J Lin, C Tang, C Chen*, W. Li*, Z Qi*

Deciphering the molecular mechanism underlying morphology transition in two-component DNA-protein cophase separation

Structure, 2025, 33 (1), 62-77.e8

4.   C Xu^#, Y Lu^#, Y Wu^#, S Yuan, J Ma, H Fu, H Wang, L Wang, H Zhang, X Yu, W Tao, C Liu, S Hu, Y Peng, W Li*, Y Li*, Y Lu*, M Li*

Sodium Ion‐Induced Structural Transition on the Surface of a DNA‐Interacting Protein

Advanced Science 2024, 11 (42), 2401838

5.   X Guan, Y Bian, Z Guo, J Zhang, Y Cao, W Li*, W Wang*

Bidirectional Allostery Mechanism in Catch-Bond Formation of CD44 Mediated Cell Adhesion

J. Phys. Chem. Lett. 2024, 15 (43), 10786-10794

6.   Y Bian, F Lv, H Pan, W Ren, W Zhang, Y Wang, Y Cao, W Li*, W Wang*

Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein. Phase Separation

JACS Au 2024, 4 (9), 3690-3704

7.   X Guan, QY Tang, W Ren, M Chen, W Wang*, PG Wolynes*, W Li*

Predicting protein conformational motions using energetic frustration analysis and AlphaFold2

Proc. Natl. Acad. Sci. U. S. A. 2024, 121 (35), e2410662121

8.  Z Xu^#, J Lu^#, D Lu, Y Li, H Lei, B Chen, W Li, B Xue, Y Cao*, W Wang*

Rapidly damping hydrogels engineered through molecular friction

Nature Commun 2024, 15 (1), 4895

9.   K Wang^#, S Zhang^#, X Zhou^#, X Yang, X Li, Y Wang, P Fan, Y Xiao, W Sun, P Zhang, W Li, S Huang*

Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by. Nanopore

Nature Methods 2023, 21, 92-101

10.   XY Guan, HY Huang, HQ Peng, YH Liu, WF Li*, W Wang*

Machine learning in molecular simulations of biomolecules

Acta Phys. Sin. 2023, 72 (24), 248708

11.   B Wen, W Zhang, Y Zhang, H Lei, Y Cao, W Li*, W Wang*

Self-Effected Allosteric Coupling and Cooperativity in Hypoxic Response Regulation with Disordered Proteins

J. Phys. Chem. Lett. 2022, 13 (39), 9201-9209.

12.   Y Zhang, M Chen, J Lu, W Li*, PG Wolynes*, W Wang*

Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis

J. Phys. Chem. B 2022, 126 (36), 6792–6801.

13.   J Lu, D Scheerer, G Haran*, W Li*, W Wang*

Role of repeated conformational transitions in substrate binding of adenylate kinase

J. Phys. Chem. B, 2022, 126 (41), 8188-8201.

14.   X Guan, C Tan, W Li*, W Wang*, D Thirumalai*

Role of water-bridged interactions in metal ion coupled protein allostery

PLoS Comput. Biol. 2022, 18 (6), e1010195.

15.   C Akil, S Ali, LT Tran, J Gaillard, W Li, K Hayashida, M Hirose, T Kato, A Oshima, K Fujishima, L Blanchoin, A Narita, RC Robinson*

Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution

Science Advances 2022, 8 (12), eabm2225.

16.   H Lei^#, Q Ma^#, W Li^#, J Wen, H Ma, M Qin, W Wang*, Y Cao

An ester bond underlies the mechanical strength of a pathogen surface protein

Nature Communications 2021, 12 (1), 5082.

17.   T Dong, T Gong, W Li*

Accurate Estimation of Solvent Accessible Surface Area for Coarse-Grained Biomolecular Structures with Deep Learning

J. Phys. Chem. B, 2021,125 (33), 9490–9498.

18.   Y Wang, X Guan, S Zhang, Y Liu, S Wang, P Fan, X Du, S Yan, P Zhang, HY Chen, W Li*, D Zhang*, S Huang*

Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A

Nature Communications, 2021, 12, 3368.

19.   J Lu, X Zhang, Y Wu, Y Sheng, W Li*, W Wang*

Energy landscape remodeling mechanism of Hsp70-chaperone-accelerated protein folding

Biophys. J. 2021, 120 (10), 1971-1983.

20.   W Zhu, J Zhang, J Wang*, W Li*, W Wang*

Enhanced sampling method with coarse graining of conformational space

Phys. Rev. E 2021, 103 (3), 032404.

21.   W Zhang, Y Cao, W Li*, W Wang*

Allostery and molecular stripping mechanism in profilin regulated actin filament growth

New J. Phys. 2021, 23, 123010.

22.   X Xu*, J Shi, J Wang*, W Li*

Long-range correlation and critical fluctuations in coevolution networks of protein sequences

Physica A, 2021, 562, 125339.

23.   Y Guo, M Werner, W Li*, JU Sommer*, VA Baulin*

Shape-Adaptive Single-Chain Nanoparticles Interacting with Lipid Membranes

Macromolecules,2019, 52 (24), 9578-9584.

24.   Wenfei Li*, Jun Wang, Jian Zhang, Shoji Takada*, and Wei Wang*
Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration,
Phys. Rev. Lett. 2019, 122, 238102.

25.   H Zorgati, M Larsson, W Ren, AYL Sim, J Gettemans, JM Grimes, Wenfei Li*, R. C. Robinson*,
The role of gelsolin domain 3 in familial amyloidosis (Finnish type)
Proc. Natl. Acad. Sci. U. S. A. 2019, 116, 13958-13963.

26.   Jianyang Kong, Jiachen Li, Jiajun Lu, Weifei Li*, Wei Wang*
Role of substrate-product frustration on enzyme functional dynamics
Phys. Rev. E 2019, 100, 052409.

27.   W. Di, X. Gao, W. Huang, Y. Sun, H. Lei, Y. Liu, W. Li, Y. Li, X. Wang, M. Qin, Z. Zhu*, Y. Cao*, W. Wang*,

Direct Measurement of Length Scale Dependence of the Hydrophobic Free Energy of a Single Collapsed Polymer Nanosphere,

Phys. Rev. Lett., 2019, 122: 047801.

28.   R. Song, X. Wu, B. Xue, Y. Yang, W. Huang, G. Zeng, J. Wang, W. Li, Y. Cao, W. Wang*, J. Lu*, H. Dong*

Principles governing catalytic activity of self-assembled short peptides

J. Am. Chem. Soc. 2018, 141 (1), 223-231.

29.   Chao Liu, Yangyang Zhang, Jian Zhang, Jun Wang, Wenfei Li*; Wei Wang*,

Interplay between translational diffusion and large-amplitude angular jumps of water molecules, 

 J. Chem. Phys. 2018, 148: 184502.

30.   Shintaroh Kubo, Wenfei Li, Shoji Takada*,

Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations,

PLoS Comput. Biol., 2017, 13(9): e1005748.

31.   Weitong Ren, Wenfei Li*; Jun Wang, Jian Zhang, Wei Wang*

Consequences of Energetic Frustration on the Ligand-Coupled Folding/Dimerization Dynamics of Allosteric Protein S100A12 ,

J. Phys. Chem. B, 2017 , 121(42): 9799-9806.

32.   Wenfei Li, Jun Wang*, Jian Zhang and Wei Wang*

Molecular simulations of metal-coupled protein folding,

Curr. Opin. Struct. Biol. 2015, 30, 25-31.

33.   Wenfei Li*, Jian Zhang, Jun Wang, and Wei Wang*

Multiscale theory and computational method for biomolecule simulations
      Acta Physica Sinica, 64, 098701 (2015) (in chinese).

34.   Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, and Hiroo Kenzaki,

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations,

Accounts of Chemical Research, 2015, 48, 3026-3035.

35.   Wenfei Li, Wei Wang* and Shoji Takada*

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains,

Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 10550-10555.

36.   Chunmei Lv^#, Xiang Gao^#, Wenfei Li^#, Bo Xue, Meng Qin, Leslie D. Burtnick, Hao Zhou, Yi Cao*, Robert C. Robinson*, Wei Wang*

Single-molecule force spectroscopy reveals force-enhanced binding of calcium ions by gelsolin

Nature Communications 2014, 5, 4623. 

37.   Chao Liu, Wenfei Li*, and Wei Wang*

Correlation of Reorientational Jumps of Water Molecules in Bulk Water

Phys. Rev. E 2013, 87, 052309.

38.   Cheng Tan, Wenfei Li*, and Wei Wang*

Localized Frustration and Binding-Induced Conformational Change in Recognition of 5sRNA by TFIIIA Zinc Finger

J. Phys. Chem. B 2013, 117, 15917-15925.

39.   Wenfei Li, Tsuyoshi Terakawa, Wei Wang* and Shoji Takada*

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot,

Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 17789-17794.

40.   Wenhui Xi, Wenfei Li*, and Wei Wang*

Template Induced Conformational Change of Amyloid-β Monomer

J. Phys. Chem. B, 2012, 116, 7398–7405.

41.   Wenfei Li, Peter G. Wolynes*, and Shoji Takada*

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 3504–3509.

42.   Wenfei Li, Meng Qin, Zuoxiu Tie, and Wei Wang*

Effects of solvents on the intrinsic propensity of peptide backbone conformations

Phys. Rev. E 2011, 84, 041933.

43.    Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-ichi Okazaki, Xin-Qiu Yao, and Shoji Takada 

CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work,

J. Chem. Theory & Comput., 2011, 7, 1979-1989.

    44.   Guanghong Zuo, Wenfei Li*, Jian Zhang,Jin Wang, Wei Wang*

Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular. Dynamics

J. Phys. Chem. B 2010, 114, 5835-5839  

     45.   Wenfei Li and Shoji Takada*

Characterizing protein energy landscape by the self-learning multiscale simulations: Application to a designed beta-hairpin,

Biophys. J. 2010, 99, 3029-3037.

     46.   Wenfei Li, Hiroaki Yoshii, Naoto Hori, Tomoshi Kameda, and Shoji Takada* ,

Multiscale methods for protein folding simulations,

Methods 2010, 52:106-114.

      47.   Wenfei Li and Shoji Takada*,

Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously,

J. Chem. Phys. 2009, 130: 214108.

      48.   Wenfei Li, Jian Zhang, Jun Wang and Wei Wang*,

Metal Coupled folding of Cys₂His₂ Zinc-finger,

J. Am. Chem. Soc. 2008, 130, 892-900.

     49.   Wenfei Li, Jian Zhang, Yu Su, Jun Wang, Meng Qin, and Wei Wang*

  Effects of Zinc Binding on the Conformational Distribution of the Amyloid-b Peptide Based on Molecular Dynamics Simulations,

 J. Phys. Chem. B. 2007, 111, 13814-13821.

50.    Wenfei Li, Jian Zhang, and Wei Wang*

Understanding the Folding and Stability of a Zinc Finger Based Full Sequence Design Protein with Replica Exchange Molecular Dynamics Simulations

    Proteins 2007, 67, 338-349.