Personal information

Activities

Employment (2)

Vanderbilt University: Nashville, Tennessee, US

2020-08-01 to present | The SC Family Dean's Faculty Fellow and Assistant Professor (Department of Chemistry | Data science institute)
Employment
Source: Self-asserted source
Zhongyue John Yang

Massachusetts Institute of Technology: Cambridge, MA, US

2018-01-06 to 2020-07-31 | Postdoctoral Associate (Chemical Engineering)
Employment
Source: Self-asserted source
Zhongyue John Yang

Education and qualifications (2)

University of California Los Angeles: Los Angeles, CA, US

2013-09 to 2017-12 | Ph.D. (Chemistry and Biochemistry)
Education
Source: Self-asserted source
Zhongyue John Yang

Nankai University: Tianjin, Tianjin, CN

2009-09 to 2013-06 | BS (Chemistry )
Education
Source: Self-asserted source
Zhongyue John Yang

Works (50 of 87)

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Interplay between Energy and Entropy Mediates Ambimodal Selectivity of Cycloadditions

Journal of Chemical Theory and Computation
2024-12-24 | Journal article
Contributors: Wook Shin; Yaning Hou; Xin Wang; Zhongyue J. Yang
Source: check_circle
Crossref

Predicting 3D Structures of Lasso Peptides

2024-10-14 | Preprint
Contributors: Xingyu Ouyang; Xinchun Ran; Han Xu; Yi-Lei Zhao; A. James Link; Zhongyue Yang
Source: check_circle
Crossref

Physics-based Modeling in the New Era of Enzyme Engineering

2024-09-10 | Preprint
Contributors: Christopher Jurich; Qianzhen Shao; Xinchun Ran; Zhongyue Yang
Source: check_circle
Crossref

Five Hypotheses on the Origins of Temperature Dependence of 77Se NMR Shifts in Diselenides

Inorganic Chemistry
2024-07-01 | Journal article
Contributors: Alexandra C. Koziel; Marco Bortoli; Matthew Tremblay; Yilun Zhao; Laura Orian; Zhongyue J. Yang; Nathan D. Schley; Janet E. Macdonald
Source: check_circle
Crossref

Predicting 3D Structures of Lasso Peptides

2024-06-13 | Preprint
Contributors: Xingyu Ouyang; Xinchun Ran; Han Xu; Yi-Lei Zhao; A. James Link; Zhongyue Yang
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Antimicrobial Lasso Peptide Cloacaenodin Utilizes a Unique TonB-Dependent Transporter to Access Susceptible Bacteria

ACS Chemical Biology
2024-04-19 | Journal article
Contributors: Drew V. Carson; Reecan J. Juarez; Truc Do; Zhongyue J. Yang; A. James Link
Source: check_circle
Crossref

EnzyKR: a chirality-aware deep learning model for predicting the outcomes of the hydrolase-catalyzed kinetic resolution

Chemical Science
2023 | Journal article
Contributors: Xinchun Ran; Yaoyukun Jiang; Qianzhen Shao; Zhongyue J. Yang
Source: check_circle
Crossref

Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis

The Journal of Physical Chemistry Letters
2023-12-21 | Journal article
Contributors: Yaoyukun Jiang; Ning Ding; Qianzhen Shao; Sebastian L. Stull; Zihao Cheng; Zhongyue J. Yang
Source: check_circle
Crossref

Mutexa: A Computational Ecosystem for Intelligent Protein Engineering

Journal of Chemical Theory and Computation
2023-11-14 | Journal article
Contributors: Zhongyue J. Yang; Qianzhen Shao; Yaoyukun Jiang; Christopher Jurich; Xinchun Ran; Reecan J. Juarez; Bailu Yan; Sebastian L. Stull; Anvita Gollu; Ning Ding
Source: check_circle
Crossref

EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation

Journal of Chemical Information and Modeling
2023-09-11 | Journal article
Contributors: Qianzhen Shao; Yaoyukun Jiang; Zhongyue J. Yang
Source: check_circle
Crossref

High‐throughput computational investigation of protein electrostatics and cavity for SAM‐dependent methyltransferases

Protein Science
2023-07 | Journal article
Contributors: Christopher Jurich; Zhongyue J. Yang
Source: check_circle
Crossref

EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation

2023-06-20 | Preprint
Contributors: Qianzhen Shao; Yaoyukun Jiang; Zhongyue Yang
Source: check_circle
Crossref

Accelerated Entropic Path Sampling with a Bidirectional Generative Adversarial Network

The Journal of Physical Chemistry B
2023-05-18 | Journal article
Contributors: Wook Shin; Xinchun Ran; Zhongyue J. Yang
Source: check_circle
Crossref

Computational Strategies for Entropy Modeling in Chemical Processes

Chemistry – An Asian Journal
2023-05-02 | Journal article
Contributors: Wook Shin; Zhongyue J. Yang
Source: check_circle
Crossref

High-Throughput Screen Reveals the Structure–Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin

ACS Central Science
2023-03-22 | Journal article
Contributors: Alina Thokkadam; Truc Do; Xinchun Ran; Mark P. Brynildsen; Zhongyue J. Yang; A. James Link
Source: check_circle
Crossref

Properties of Configurationally Stable Atropoenantiomers in Macrocyclic Natural Products and the Chrysophaentin Family

Accounts of Chemical Research
2023-02-21 | Journal article
Contributors: Carole A. Bewley; Gary A. Sulikowski; Zhongyue J. Yang; Giuseppe Bifulco; Hyo-Moon Cho; Christopher R. Fullenkamp
Source: check_circle
Crossref

LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling

Journal of Chemical Information and Modeling
2023-01-23 | Journal article
Contributors: Reecan J. Juarez; Yaoyukun Jiang; Matthew Tremblay; Qianzhen Shao; A. James Link; Zhongyue J. Yang
Source: check_circle
Crossref

Data-driven enzyme engineering to identify function-enhancing enzymes

Protein Engineering, Design and Selection
2023-01-21 | Journal article
Contributors: Yaoyukun Jiang; Xinchun Ran; Zhongyue J Yang
Source: check_circle
Crossref

A High-Throughput Screen Reveals the Structure-Activity Relationship of the Antimicrobial Lasso Peptide Ubonodin

2022-12-13 | Preprint
Contributors: Alina Thokkadam; Truc Do; Xinchun Ran; Mark P. Brynildsen; Zhongyue J. Yang; A. James Link
Source: check_circle
Crossref

Convergence in determining enzyme functional descriptors across Kemp eliminase variants

Electronic Structure
2022-12-01 | Journal article
Contributors: Yaoyukun Jiang; Sebastian L Stull; Qianzhen Shao; Zhongyue J Yang
Source: check_circle
Crossref

The effect of zero‐point energy in simulating organic reactions with post‐transition state bifurcation

Journal of Physical Organic Chemistry
2022-11 | Journal article
Contributors: Matthew T. Tremblay; Zhongyue J. Yang
Source: check_circle
Crossref

IntEnzyDB: an Integrated Structure–Kinetics Enzymology Database

Journal of Chemical Information and Modeling
2022-11-28 | Journal article
Contributors: Bailu Yan; Xinchun Ran; Anvita Gollu; Zihao Cheng; Xiang Zhou; Yiwen Chen; Zhongyue J. Yang
Source: check_circle
Crossref

LassoHTP: a High-throughput Computational Tool for Lasso Peptide Structure Construction and Modeling

2022-07-13 | Preprint
Contributors: Reecan J. Juarez; Matthew Tremblay; Yaoyukun Jiang; Qianzhen Shao; A. James Link; Zhongyue Yang
Source: check_circle
Crossref

IntEnzyDB: an Integrated Structure-Kinetics Enzymology Database

2022-07-05 | Preprint
Contributors: Bailu Yan; Xinchun Ran; Anvita Gollu; Zihao Cheng; Xiang Zhou; Yiwen Chen; Zhongyue Yang
Source: check_circle
Crossref

ARMer: A Python Library for Adaptive Resource Allocation in High-Throughput Workflow

2022-06-30 | Preprint
Contributors: Qianzhen Shao; Zhongyue Yang
Source: check_circle
Crossref

Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer

Journal of the American Chemical Society
2022-06-29 | Journal article
Contributors: Beverly Fu; Azadeh Nazemi; Benjamin J. Levin; Zhongyue Yang; Heather J. Kulik; Emily P. Balskus
Source: check_circle
Crossref

Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch

The Journal of Physical Chemistry B
2022-05-12 | Journal article
Contributors: Zhongyue Yang; Natalia Hajlasz; Heather J. Kulik
Source: check_circle
Crossref

Molecular Dynamics-Derived Descriptor Informs the Impact of Mutation on the Catalytic Turnover Number in Lactonase Across Substrates

The Journal of Physical Chemistry B
2022-04-07 | Journal article
Contributors: Yaoyukun Jiang; Bailu Yan; Yu Chen; Reecan J. Juarez; Zhongyue J. Yang
Source: check_circle
Crossref

Self-Immolative Hydroxybenzylamine Linkers for Traceless Protein Modification

Journal of the American Chemical Society
2022-04-06 | Journal article
Contributors: Douglas A. Rose; Joseph W. Treacy; Zhongyue J. Yang; Jeong Hoon Ko; K. N. Houk; Heather D. Maynard
Source: check_circle
Crossref

EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling

Journal of Chemical Information and Modeling
2022-02-14 | Journal article
Contributors: Qianzhen Shao; Yaoyukun Jiang; Zhongyue J. Yang
Source: check_circle
Crossref

EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling

2021-11-24 | Other
Contributors: Qianzhen Shao; Yaoyukun Jiang; Zhongyue Yang
Source: check_circle
Crossref

Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path

The Journal of Physical Chemistry Letters
2021-11-04 | Journal article
Contributors: Zhi-Xin Qin; Matthew Tremblay; Xin Hong; Zhongyue J. Yang
Source: check_circle
Crossref

The Effect of Zero-Point Energy in Simulating Organic Reactions with Post-Transition State Bifurcation

2021-10-25 | Preprint
Contributors: Matthew Tremblay; Zhongyue John Yang
Source: check_circle
Crossref

The Effect of Zero-Point Energy in Simulating Organic Reactions with Post-Transition State Bifurcation

2021-10-25 | Other
Contributors: Matthew Tremblay; Zhongyue John Yang
Source: check_circle
Crossref

Rate-Perturbing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling

The Journal of Physical Chemistry B
2021-09-30 | Journal article
Contributors: Bailu Yan; Xinchun Ran; Yaoyukun Jiang; Sarah K. Torrence; Li Yuan; Qianzhen Shao; Zhongyue J. Yang
Source: check_circle
Crossref

Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path

2021-09-23 | Preprint
Contributors: Zhi-Xin Qin; Matthew Tremblay; Xin Hong; Zhongyue Yang
Source: check_circle
Crossref

Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path

2021-09-23 | Other
Contributors: Zhi-Xin Qin; Matthew Tremblay; Xin Hong; Zhongyue Yang
Source: check_circle
Crossref

Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase

The Journal of Physical Chemistry B
2021-07-22 | Journal article
Contributors: Zhongyue Yang; Heather J. Kulik
Source: check_circle
Crossref

EnzyHTP: A High-throughput Enzyme Modeling Workflow

2021-07-19 | Software
Source: Self-asserted source
Zhongyue John Yang

Quantifying the Long‐Range Coupling of Electronic Properties in Proteins with ab initio Molecular Dynamics**

Chemistry–Methods
2021-07-19 | Journal article
Part of ISSN: 2628-9725
Part of ISSN: 2628-9725
Source: Self-asserted source
Zhongyue John Yang

Die Evolution des Diels‐Alder‐Reaktionsmechanismus seit den 1930er Jahren: Woodward, Houk zusammen mit Woodward und der Einfluss der Computerchemie auf das Verständnis von Cycloadditionen

Angewandte Chemie
2021-06 | Journal article
Contributors: Kendall N. Houk; Fang Liu; Zhongyue Yang; Jeffrey I. Seeman
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Crossref

Evolution of the Diels–Alder Reaction Mechanism since the 1930s: Woodward, Houk with Woodward, and the Influence of Computational Chemistry on Understanding Cycloadditions

Angewandte Chemie International Edition
2021-06 | Journal article
Contributors: Kendall N. Houk; Fang Liu; Zhongyue Yang; Jeffrey I. Seeman
Source: check_circle
Crossref

IntEnzyDB: An Integrated Structure-Function Enzymology Database

2021-06-01 | Data set
Source: Self-asserted source
Zhongyue John Yang

Rate-enhancing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling

Source: Self-asserted source
Zhongyue John Yang
grade
Preferred source (of 2)‎

Ionization behavior of nanoporous polyamide membranes

Proceedings of the National Academy of Sciences
2020-12 | Journal article
Contributors: Cody L. Ritt; Jay R. Werber; Mengyi Wang; Zhongyue Yang; Yumeng Zhao; Heather J. Kulik; Menachem Elimelech
Source: check_circle
Crossref

Mechanisms and Dynamics of Reactions Involving Entropic Intermediates

Trends in Chemistry
2019 | Journal article
Source: Self-asserted source
Zhongyue John Yang

Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation

Reaction Chemistry & Engineering
2019 | Journal article
Contributors: Zhongyue Yang; Rimsha Mehmood; Mengyi Wang; Helena W. Qi; Adam H. Steeves; Heather J. Kulik
Source: check_circle
Crossref

Harnessing fluoroacetate dehalogenase for defluorination of fluorocarboxylic acids: in silico and in vitro approach.

Environment international
2019-07-15 | Journal article
Contributors: Yanwei Li; Yue Y; Zhang H; Yang Z; Wang H; Tian S; Wang JB; Zhang Q; Wang W
Source: Self-asserted source
Zhongyue John Yang

Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases

The Journal of Physical Chemistry Letters
2019-07-05 | Journal article
Contributors: Zhongyue Yang; Fang Liu; Adam H. Steeves; Heather J. Kulik
Source: check_circle
Crossref

Molecular dynamics of the intramolecular 1, 3-dipolar ene reaction of a nitrile oxide and an alkene: non-statistical behavior of a reaction involving a diradical intermediate

Molecular Physics
2019-06-18 | Journal article
Contributors: Yanmin Yu; Zhongyue Yang; K. N. Houk
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Crossref
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Peer review (23 reviews for 13 publications/grants)

Review activity for ACS omega. (1)
Review activity for Biochemistry. (2)
Review activity for Biotechnology advances. (2)
Review activity for Chemosphere. (1)
Review activity for Journal of chemical education. (1)
Review activity for Journal of chemical information and modeling. (2)
Review activity for Journal of chemical theory and computation : (1)
Review activity for Journal of the American Chemical Society. (6)
Review activity for Nature Catalysis. (1)
Review activity for Nature chemistry. (1)
Review activity for Nature communications (2)
Review activity for The journal of physical chemistry letters. (1)
Review activity for The journal of physical chemistry. (2)