Publications

Zhang, Y., Xiao, J., Wang, S., Zhu, T., and Zhang, J. Z. H. The Atomic Density-Based Tight-Binding (aTB) Model: A Robust and Accurate Semiempirical Method Parametrized for H–Ra; Applied to Structures, Vibrational Frequencies, Noncovalent Interactions, and Excited States. J. Chem. Theory Comput. 21, 3410–3425 (2025)

Wang, Y., Takaba, K., Chen, M. S., Wieder, M., Xu, Y., Zhu, T., Zhang, J. Z. H., Nagle, A., Yu, K., Wang, X., Cole, D. J., Rackers, J. A., Cho, K., Greener, J. G., Eastman, P., Martiniani, S., and Tuckerman, M. E. On the Design Space Between Molecular Mechanics and Machine Learning Force Fields. Appl. Phys. Rev. 12, 021304 (2025)

Xia, S., Gu, Y., and Zhang, Y. Normalized protein–ligand distance likelihood score for end-to-end blind docking and virtual screening. J. Chem. Inf. Model. 65, 1101–1114 (2025)

Miao, T., Zhi, F., Yang, X., Yuan, Z., Zhang, C., Feng, Y., Wei, H., Jiang, H., Gao, B., and Zhang, L. Break through the thermostability of glucose oxidase in extremely thermal environments with a novel dynamic ensemble design protocol. Process Biochem. 148, 55-62 (2025)

Gong, L., Liu, F., Zhang, C., Ming, Y., Mou, Y., Yuan, Z.T., Jiang, H., Gao, B., Lu, F., and Zhang, L. LICEDB: Light industrial core enzyme database for industrial applications and AI enzyme design. Database 2025, baaf001 (2025)

Yuan, Z., Fang, B., He, Q., Wei, H., Jian, H., and Zhang, L. Molecular dynamics study of the structure and mechanical properties of spider silk proteins. Biomacromolecules 26, 601 - 608 (2025)

Li, L., et al. Dimeric natural product panepocyclinol A inhibits STAT3 via di-covalent modification. Acta Pharm. Sin. B 15, 409-423 (2025)

Li, P., Pu, T., and Mei, Y. FEP-SPell-ABFE: An open-source automated Alchemical absolute binding free-energy calculation workflow for drug discovery. J. Chem. Inf. Model. (2025)

Yan, S. and Schlick, T. Heterogeneous and multiple conformational transition pathways between pseudoknots of the SARS-CoV-2 frameshift element. Proc. Natl. Acad. Sci. U.S.A. 122, e2417479122 (2025)

Wieczór, M and Schlick, T. Phase Space Invaders’ podcast episode with Tamar Schlick: a trajectory from mathematics to biology. Biophys. Rev. 17, 15–23 (2025)

Lee, S., Yan, S., Dey, A., Laederach, A., and Schlick, T. A cascade of conformational switches in SARS-CoV-2 frameshifting: Coregulation by upstream and downstream elements. Biochemistry 64, 953–966 (2025)

Li, Z., Portillo-Ledesma, S., Janani, M., and Schlick, T. Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers. J. Chem. Phys. 162, 094107 (2025)

Simkó, I., Felker, P.M., and Bačić, Z. H₂O trimer: Rigorous 12D quantum calculations of intermolecular vibrational states, tunneling splittings, and low-frequency spectrum. J. Chem. Phys. 162, 034301 (2025)

Li, B., Xiao, J., Gao, Y., Zhang, J. Z. H., and Zhu, T. Transition state searching accelerated by neural network potential. J. Chem. Inf. Model. 65, 2297–2303 (2025)

Muhammad, D., Xia, W., Sun, Z., and  Zhang, J. Z. H. Molecular glue-augmented E2-ubiquitin recognition from a computational approach. Int. J. Biol. Macromol. 306, 141454 (2025)

Zhang, Y., Xia, W., Xiao J., and Zhang, J. Z. H. Toward quantum chemical accuracy in absolute protein–ligand binding free energy calculation via quantum fragment method. J. Chem. Theory Comput.  21, 2129–2139 (2025)

Poe, D., Abranches, D. O., Wang., X., Klein, J., Dean, W., Hansen, B. B., Doherty, B., Fraenza, C., Gurkan, C., Sangoro, J. R., Tuckerman, M., Greenbaum, S.G., and Maginn, E. J. Structural and dynamic heterogeneity of deep eutectic solvents composed of choline chloride and ortho-phenol derivatives. J. Phys. Chem. B 129, 1360–1375 (2025)

Lu, J., He, Y., Li, Y., Chen, X., Li, H., Chen, X., Xu, J., Chen, H., Wang, Y., He, X., Liu, S., and Chen, L. Exploring bifunctional molecules for anti-SARS-CoV-2 and anti-inflammatory activity through structure-based virtual screening, SAR investigation, and biological evaluation. Int. J. Biol. Macromol. 287, 138529 (2025)

Wang, X., Zhao, C., Yang, M., Baek, J.-H., Meng, Z., Sun, B., Yuan, A., Baek, J.-B., He, X., Jiang, Y., and Zhu, M. Bioinspired photothermal metal-organic framework cocrystal with ultra-fast water transporting channels for solar-driven interfacial water evaporation. Small 21, 2407665 (2025)

Mou, Y., Jiang, Y., He, X., Zhang, L., and Yang, J. Dynamic modulation of ions solvation sheath by butyramide as molecular additives in aqueous batteries. J. Phys. Chem. B 129, 423–434 (2025)

Wang, X., Zhang, Z.-Y., He, X., Liu, Z., and Sun, Z. True dynamics of pillararene host–guest binding. J. Chem. Theory Comput. 21, 241–253 (2025)

Wang, X., Xiong, D., Zhang, Y., Zhai, J., Gu, Y.-C., and He, X. The evolution of the Amber additive protein force field: History, current status, and future. J. Chem. Phys. 162, 030901 (2025)

Liu, Y., Liu, J., Xia, Y., Chen, W., Li, Y., He, X., and Yang, Q., Structure-based virtual screening of novel chitin synthase inhibitors for the control of Phytophthora sojae. Pest Manag. Sci. 81, 777-785 (2025)

Zhou, X., Li, L., Xue, J., Wang, F., and He, X. Theoretical study on the kinetics of secondary oxygen addition reactions for n-butyl radicals. J. Phys. Chem. A 129, 1441–1451 (2025)

Xu, Y., Ni, H., Zhao, F., Gao, Q., Zhao, Z., Chang, C.-H., Huo, Y., Hu, S., Zhang, Y., Grovu, R., He, H., Zhang, J. Z. H., and Wang, Y. Molecular dynamics and machine learning unlock possibilities in beauty design—A perspective. AIP Adv. 15, 010601 (2025)

Liu, J., Luo, S., Xu, X., Zhang, E., Liang, H., Zhang, J. Z. H., and Duan, L. Evaluating the synergistic effects of multi-epitope nanobodies on BA.2.86 variant immune escape. J. Phys. Chem. Letter 16, 396–405 (2025)

Huang, E., Liu, S., Zhou, X., Zhong, L., Ma, S., Wang, R., Li, H., Yang, J., He, X., Dong, W., and Yang, X. Vibrational spectroscopy and structural characterization of neutral and cationic hydroxyacetone. J. Mol. Struct. 1321, 139871 (2025)

Zhang, C., Feng, Y., Zhu, Y., Gong, L., Wei, H., and Zhang, L. NAC4ED: A high-throughput computational platform for the rational design of enzyme activity and substrate selectivity. mLife 3, 505-514 (2024)

Hu, F., Zhang, Y., Li, P., Wu, R., and Xia, F. Development of accurate force fields for mg²⁺ and triphosphate interactions in ATP·mg²⁺ and GTP·mg²⁺ complexes. J. Chem. Theory Comput. 20, 10553–10563 (2024)

Hong, R. S., Alagbe, B. D., Mattei, A., Sheikh, A. Y., and Tuckerman, M. E. Enhanced and efficient predictions of dynamic ionization through constant-pH adiabatic free energy dynamics. J. Chem. Theory Comput. 20, 10010–10021 (2024)

Prado, D. M., Robledo, A., Hightower, K., Jahng, A., Doherty, B., Poling, K., Tuckerman, M., and Burda, C. Breakthrough conductivity enhancement in deep eutectic solvents via Grotthuss-type proton transport. Adv. Mater. Interfaces 11, 2400508 (2024) 

Chan, E. J. and Tuckerman, M. E. Polymorph sampling with coupling to extended variables: enhanced sampling of polymorph energy landscapes and free energy perturbation of polymorph ensembles. Acta Cryst. 80, 575-594 (2024)

Zhou, B.-R., Feng, H., Huang, F., Zhu, I., Portillo-Ledesma, S., Shi, D., Zaret, K. S., Schlick, T., Landsman, D., Wang, Q., and Bai, Y. Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4. Mol. Cell 84, 3061-3079.e10 (2024)

Felker, P.M., Simkó, I., and Bačić, Z. Intermolecular bending states and tunneling splittings of water trimer from rigorous 9D quantum calculations: I. methodology, energy levels, and low-frequency spectrum. J. Phys. Chem. A 128, 8170–8189 (2024)

Gan, Z., Feng, J., Yin, J., Huang, J., Wang, B., and Zhang, J. Z. H. Diverse mechanisms for the aromatic hydroxylation: Insights into the mechanisms of the coumarin hydroxylation by CYP2A6. ACS Catal. 14, 16277–16286 (2024)

Zheng, L., Zeng, Z., Zhao. Y., Liu, X., Huai, Z., Zhang, X., Sun, Z., and Zhang, J. Z. H. HSADab: A comprehensive database for human serum albumin. Int. J. Biol. Macromol. 277, 134289 (2024)

Sun. H., Sun, Z., and Wang, X.-B. Probing noncovalent interaction strengths of host-guest complexes using negative ion photoelectron spectroscopy. Chem. Eur. J. 30, e202402766 (2024)

Li, X.-T., Mi, S., Xu, Y., Li, B.-W., Zhu, T., and Zhang, J. Z. H. Discovery of new synthetic routes of amino acids in prebiotic chemistry. JACS Au 4, 4757–4768 (2024)

Li, Y., Chen, Y., and He, X. Teaching spin symmetry while learning neural network wave functions. Nat. Comput. Sci. 4, 884–885 (2024)

Huang, K., Duan, L., and Zhang, J. Z. H. From implicit to explicit: An interaction-reorganization approach to molecular solvation energy. J. Chem. Theory Comput. 20, 10961–10971 (2024)

Liu, X., Pang, K., Wu, H., Wang, X., Zhang, J. Z. H., and Sun, Z. All-atom perspective of the DENV-3 methyltransferase inhibition mechanism. J. Phys. Chem. B 128, 12358–12367 (2024)

Xu, Y., Liu, X., Xia, W., Ge, J., Ju, C.-W., Zhang, H., and Zhang, J. Z. H. ChemXTree: A feature-enhanced graph neural network-neural decision tree framework for ADMET prediction. J. Chem. Inf. Model. 64, 8440–8452 (2024)

Jiang, Y., Xiong, D., Wan,, Yang, J., and He, X. Mechanism-guided rational design of anode coatings for aqueous zinc ion batteries. ChemPhysChem 25, e202400231 (2024)

Liu, Z., Brian, D., and Sun, X. PyCTRAMER: A Python package for charge transfer rate constant of condensed-phase systems from Marcus theory to Fermi’s golden rule. J. Chem. Phys. 161, 0641012024 (2024)

Zhang, Z., Ke, D., Jin, C., Zhou, W., Pan, X., Zhang, Y., Wang, X., Xiao, X., and Ji, C. MacGen: A web server for structure-based macrocycle design. J. Chem. Inf. Model. 64, 9048–9055 (2024)

Galanakis, N. and Tuckerman, M. E. Rapid prediction of molecular crystal structures using simple topological and physical descriptors. Nat. Commun. 15, 9757 (2024)

Hunnisett, L. M., et al. The seventh blind test of crystal structure prediction: Structure generation methods. Acta Cryst. 80, 517-547 (2024)

Dey, A., Yan, S., Schlick, T., and Laederach, A. Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses. RNA 30, 1437-1450 (2024)

Li, J., Vindel-Zandbergen, P., Li, J., Felker, P.M., and Bačić, Z. HF trimer: A new full-dimensional potential energy surface and rigorous 12D quantum calculations of vibrational states. J. Phys. Chem. A 128, 9707-9720 (2024)

Li, J., Vindel-Zandbergen, P., Li, J., Felker, P.M., and Bačić, Z. HF trimer: A new full-dimensional potential energy surface and rigorous 12D quantum calculations of vibrational states. J. Phys. Chem. A 128, 9707-9720 (2024)