2025

26. Yue C⁺, Xie S⁺, Ye S*, Li ZL*. Biological Condensate Growth: Examining the Impact of Solute Crowder on Size Expansion. Biomacromolecules 2025.

2024

25. Li T, Ren X, Luo X, Wang Z, Li ZL, Luo X, Shen J, Li Y, Yuan D, Nussinov R, Zeng X, Shi J, Cheng F. A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection. Nat Commun. 2024 Aug 30;15(1):7538.

24. Xie S, Yue C, Ye S, Li ZL*. Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complexes through fuzzy interaction and mesoscale condensation. Phys Chem Chem Phys. 2024 Mar 27;26(13):10408-10418.

23. Li ZL*, Yue C, Xie S, Shi S, Ye S. Computational insights into the conformational transition of STING: Mechanistic, energetic considerations, and the influence of crucial mutations. J Mol Graph Model. 2024 Jun;129:108764. 

2023

22. Li ZL*, Buck M*. A proteome-scale analysis of vertebrate protein amino acid occurrence: thermoadaptation shows a correlation with protein solvation but less so with dynamics. Proteins 2023 Jan;91(1):3-15.   

2022

21. Li ZL*, Mattos C, Buck M*. Computational studies of the principle of dynamic-change-driven protein interactions. Structure  2022 Jun 2;30(6):909-916.e2.

20. Li ZL*, Buck M*. Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity. Computational and Structural Biotechology Journal  2022:20:6078-6086

19. Basavarajappa S, Liu A, Bruchez A, Li, ZL, Suzart V, Liu Z, Xiao T, Buck M, Ramakrishnan P. Trimeric receptor binding domain of SARS CoV-2 acts as a potent inhibitor of ACE2 receptor mediated viral entry structure. iScience 2022 Aug 19;25(8):104716

18.  Pshetitsky, Yaron; Mendelman, Netanel; Li, ZL; Zerbetto, Mirco; Buck, Matthias; Meirovitch, Eva. Microsecond MD Simulations of the Plexin-B1 RBD: N-H. Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry. The Journal of Physical Chemistry B. 2022, 126, 34, 6396–6407

17. Mendelman, Netanel; Pshetitsky, Yaron; Li, ZL; Zerbetto, Mirco; Buck, Matthias; Meirovitch, Eva. Microsecond MD Simulations of the Plexin-B1 RBD: 2. N-H Probability Densities and Conformational Entropy in Ligand-Free, Rac1-Bound, and Dimer RBD. The Journal of Physical Chemistry B. 2022 Sep 1;126(34):6408-6418

Before joining TJU

16. Li ZL, Buck M. Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2. Biophys J. 2021 Jul 20;120(14):2828-2837. 

15. Li ZL*, Buck M*. Beyond history and "on a roll": The list of the most well-studied human protein structures and overall trends in the protein data bank. Protein Sci. 2021 Apr;30(4):745-760.

14. Packer MR, Parker JA, Chung JK, Li ZL, Lee YK, Cookis T, Guterres H, Alvarez S, Hossain MA, Donnelly DP, Agar JN, Makowski L, Buck M, Groves JT, Mattos C. Raf promotes dimerization of the Ras G-domain with increased allosteric connections. Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):e2015648118.

13. Li ZL, Müller-Greven J, Kim S, Tamagnone L, Buck M. Plexin-Bs enhance their GAP activity with a novel activation switch loop generating a cooperative enzyme. Cell Mol Life Sci. 2021 Feb;78(3):1101-1112.

12. Li ZL*, Buck M*. Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface. J Chem Inf Model. 2020 Jan 27;60(1):306-315.

11. Cao S, Chung S, Kim S, Li ZL, Manor D, Buck M. K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function. J Biol Chem. 2019 Apr 26;294(17):7068-7084.

10. Li ZL, Buck M. Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein-Protein Interactions. J Chem Theory Comput. 2019 Aug 13;15(8):4318-4331.

9. Babinchak, W.M., Li, Z.L. & Buck, M. Keys to Amyloid City: Computation and NMR Reveal Potential TDP-43 ALS Intermediates. Biophysical Journal.  2018, 115, 1625-1627.

8. Li ZL, Prakash P, Buck M. A "Tug of War" Maintains a Dynamic Protein-Membrane Complex: Molecular Dynamics Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane. ACS Cent Sci. 2018 Feb 28;4(2):298-305.

7. Li ZL* Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1. Chin. Phys. B. 2018, 27, 038703.

6. Shengjuler D, Chan YM, Sun S, Moustafa IM, Li ZL, Gohara DW, Buck M, Cremer PS, Boehr DD, Cameron CE. The RNA-Binding Site of Poliovirus 3C Protein Doubles as a Phosphoinositide-Binding Domain. Structure. 2017 Dec 5;25(12):1875-1886.e7.

5. Li ZL, Buck M. Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology. Structure. 2017 Apr 4;25(4):679-689.e2.

4. Li ZL, Cao, S, Buck, M.  K-Ras at Anionic Membranes: Orientation, Orientation…Orientation. Recent Simulations and Experiments. Biophys. J. 2016, 110, 1033-1035.

3. Li ZL, Ding HM, Ma YQ. Interaction of peptides with cell membranes: insights from molecular modeling. J Phys Condens Matter. 2016 Mar 2;28(8):083001.

2. Li ZL, Wang, J. J., Ding, H.M. &Ma, Y.Q. (2014) Influence of different membrane environments on the behavior of cholesteroll. RSC Advance, 4, 53090-53096.

1. Li ZL, Ding HM, & Ma YQ. (2013) Translocation of polyarginines and conjugated nanoparticles across asymmetric membranes. Soft Matter, 9, 1281-1286.