Publications

Jurich, C.; Shao, Q.; Ran, X.; Yang, Z. J.*, Physics-based Modeling in the New Era of Computational Enzyme Engineering Nature Computational Science. 2025 (5) 279–291 (Invited Perspective)

Shao, Q.; Hollenbeak, A. C.; Jiang, Y.; Bachmann, B. O.*; Yang, Z. J.*, SubTuner Leverages Physics-based Modeling to Complement AI in Enzyme Engineering towards Non-Native Substrates Chem Catalysis. 2025 (5) 101334

Ouyang, X.; Ran, X.; Xu, Han; Zhao, Y.-L.*; Link, A. J.*; Yang, Z. J.*, LassoPred: a Tool to Predict the 3D Structure of Lasso Peptides Nature Communications . 2025 (16) 5497

Ding, N.; Jiang, Y.; Ge, Robbie; Ran, Xinchun; Yang, Z. J.*, Enhance Cold Adaptation of Bidomain Amylases via High-throughput Computational Engineering Angewandte Chemie International Edition. 2025 e202505991 (Selected as Hot Paper)

Wei, G.; Ran, X.; Al-Abssi, R.; Yang, Z. J.*, Finding the Dark Matter: Large Language Model-based Enzyme Kinetic Data Extractor and Its Validation Protein Science. 2025 (34) e70251 (Selected as the Journal Cover)

Cunningham, K. M.; Shin, W.; Yang, Z. J.*, Computational Studies of Enzymes for C–F Bond Degradation and Functionalization ChemPhysChem. 2025 (26) e202401130

Ding, N.*; Jiang, Y.; Lee, S.; Cheng, Z.; Ran, X.; Ding, Y.; Ge, R.; Zhang, Y.*; Yang, Z. J.*, Enzyme Miniaturization: Revolutionizing Future Biocatalysts Biotechnology Advances. 2025 (82) 108598

Ge, R.; Ding, N.; Jiang, Y.; Yang, Z. J.*, Linker-Mediated Domain Separation Enhances Cold Adaptation in Cellulases Protein Science. 2025 (34) e70198

Shin, W.; Hou, Y.; Wang, X.; Yang, Z. J.*, Interplay between Energy and Entropy Mediates Ambimodal Selectivity of Cycloadditions Submitted. 2024

Koziel, A.; Bortoli, M.; Tremblay, M.; Zhao, Y.; Orian, L.; Yang, Z. J.; Schley, N.; Macdonald, J., Five Hypotheses on the Origins of Temperature Dependence of 77Se NMR Shifts in Diselenides 2024 (63) 12063–12072

Carson, D., Juarez, R., Do, T., Yang, Z. J., Link, A. J., The Antimicrobial Lasso Peptide Cloacaenodin Utilizes a Unique TonB-dependent Transporter to Access Susceptible Bacteria ACS Chemical Biology. 2024 (19) 981-991

Long T., LI D., Jiang Y., Schmiege P., Yang Z. J., McDonald J. G., Li X., Structural Mechanism and Inhibition of Human Phosphatidylserine Synthesis Cell. 2024 (Accepted manuscript)

Spiga Luisella, Fansler T., Perera R., Shealy G., Munneke J., David E., Torres P., Lemoff Andrew, Ran Xinchun, Richardson L., Pudlo Nicholas, Martens C., Folta-Stogniew Ewa, Yang Zhongyue (John), Skaar Eric P., Byndloss X., Chazin J., Zhu Wenhan, Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection Cell Host & Microbe. 2023 Oct 11; 31 (10) p. 1639-1654.e10

Shao Qianzhen, Jiang Yaoyukun, Yang Zhongyue (John), EnzyHTP: Computational Directed Evolution with Adaptive Resource Allocation Journal of Chemical Information and Modeling. 2023

Ran Xinchun, Jiang Yaoyukun, Shao Qianzhen, Yang Zhongyue (John), EnzyKR: A Chirality-Aware Deep Learning Model for Predicting the Outcomes of the Hydrolase-Catalyzed Kinetic Resolution Chemical Science. 2023

Yang Zhongyue (John), Shao Qianzhen, Jiang Yaoyukun, Jurich Christopher, Ran Xinchun, Juarez Reecan, Yan Bailu, Stull Sebastain, Gollu Anvita, Ding Ning, Mutexa: A Computational Ecosystem for Intelligent Protein Engineering Journal of Chemical Theory and Computation. 2023 Oct 12;

Jurich Christopher, Yang Zhongyue (John), High-Throughput Computational Investigation of Protein Electrostatics and Cavity for SAM-Dependent Methyltransferases Protein Science. 2023 32 (7) e4690

Bewley Carole A., Sulikowski Gary A., Yang Zhongyue (John), Bifulco Giuseppe, Cho Hyo-Moon, Fullenkamp Christopher R., Properties of Configurationally Stable Atropoenantiomers in Macrocyclic Natural Products and the Chrysophaentin Family Account of Chemical Research. 2023 Feb 2; 56 (4) 414–424

Thokkadam Alina, Do Truc, Ran Xinchun, Brynildsen Mark P., Yang Zhongyue (John), Link A. James, High-Throughput Screen Reveals the Structure–Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin ACS Central Science. 2023 Mar 1; 9 (3) 540–550

Shin Wook, Yang Zhongyue (John), Computational Strategies for Entropy Modeling in Chemical Processes Chemistry: An Asian Journal. 2023 Mar 2; 18 (9) e202300117

Juarez Reecan, Jiang Yaoyukun, Tremblay Matthew, Shao Qianzhen, Link A. James, Yang Zhongyue (John), LassoHTP: a High-throughput Computational Tool for Lasso Peptide Structure Construction and Modeling Journal of Chemical Information and Modeling. 2023 63 (2) 522–530

Shin Wook, Ran Xinchun, Wang Xin, Yang Zhongyue (John), Accelerated Entropic Path Sampling Elucidates Entropic Effects in Mediating the Ambimodal Selectivity of NgnD-Catalyzed Diels–Alder Reaction J. Phys. Chem. B. 2023 127 (19) 4254–4260

Bewley Carole, Sulikowski Gary, Yang Zhongyue (John), Bifulco Giuseppe, Shape matters – conformational chirality and atropisomerism macrocyclic natural products (submitted). 2022

Jiang Yaoyukun, Stull Sebastian L., Shao Qianzhen, Yang Zhongyue (John), Convergence in Determining Enzyme Functional Descriptors across Kemp Eliminase Variants Electronic Structure. 2022 4 (4) 044007

Jiang Yaoyukun, Yan Bailu, Chen Yu, Juarez Reecan J., Yang Zhongyue (John), Molecular Dynamics-Derived Descriptor Informs the Impact of Mutation on the Catalytic Turnover Number in Lactonase Across Substrates The Journal of Physical Chemistry B. 2022 126 (13) 2486-2495

Jiang Yaoyukun, Ran Xinchun, Yang Zhongyue (John), Data-Driven Enzyme Engineering to Identify Function-Enhancing Enzymes Protein Engineering, Design and Selection. 2022 gzac009

Yan Bailu, Ran Xinchun, Gollu Anvita, Cheng Zihao, Zhou Xiang, Chen Yiwen, Yang Zhongyue J., IntEnzyDB: an Integrated Structure-Kinetics Enzymology Database Journal of Chemical Information and Modeling. 2022 62 (22) 5841–5848

Tremblay Matthew T., Yang Zhongyue (John), The effect of zero-point energy in simulating organic reactions with post-transition state bifurcation Journal of Physical Organic Chemistry. 2022 e4322

Shao Qianzhen, Jiang Yaoyukun, Yang Zhongyue (John), EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling Journal of Chemical Information and Modeling. 2022 62 (3) 647–655

Wang Xin, Zhang Chun, Jiang Yaoyukun, Wang Wen, Zhou Yuan, Chen Yu, Zhang Bo, Tan Ren Xiang, Ge Hui Ming, Yang Zhongyue (John), Liang Yong, Influence of Water and Enzyme on the Post-Transition State Bifurcation of NgnD-Catalyzed Ambimodal [6+4]/[4+2] Cycloaddition Journal of the American Chemical Society. 2021 143 (49) 21003-21009

Qin Zhi-Xin, Tremblay Matthew, Hong Xin, Yang Zhongyue (John), Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path The Journal of Physical Chemistry Letter. 2021 43 (12) 10713–10719

Yan Bailu, Ran Xinchun, Jiang Yaoyukun, Torrence Sarah K., Li Yuan, Shao Qianzhen, Yang Zhongyue (John), Rate-Perturbing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling The Journal of Physical Chemistry B. 2021 (125) 10682–10691