Publications

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