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Zhongyue John Yang - Publications

Affiliations: 
Vanderbilt University, Nashville, TN 
Area:
Computational Enzymology
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48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Jiang Y, Ding N, Shao Q, Stull SL, Cheng Z, Yang ZJ. Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis. The Journal of Physical Chemistry Letters. 14: 11480-11489. PMID 38085952 DOI: 10.1021/acs.jpclett.3c02444  0.724
2023 Ran X, Jiang Y, Shao Q, Yang ZJ. EnzyKR: a chirality-aware deep learning model for predicting the outcomes of the hydrolase-catalyzed kinetic resolution. Chemical Science. 14: 12073-12082. PMID 37969577 DOI: 10.1039/d3sc02752j  0.701
2023 Yang ZJ, Shao Q, Jiang Y, Jurich C, Ran X, Juarez RJ, Yan B, Stull SL, Gollu A, Ding N. Mutexa: A Computational Ecosystem for Intelligent Protein Engineering. Journal of Chemical Theory and Computation. PMID 37828731 DOI: 10.1021/acs.jctc.3c00602  0.677
2023 Shao Q, Jiang Y, Yang ZJ. EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation. Journal of Chemical Information and Modeling. PMID 37611241 DOI: 10.1021/acs.jcim.3c00618  0.689
2023 Shin W, Ran X, Yang ZJ. Accelerated Entropic Path Sampling with a Bidirectional Generative Adversarial Network. The Journal of Physical Chemistry. B. 127: 4254-4260. PMID 37133810 DOI: 10.1021/acs.jpcb.3c01202  0.315
2023 Juarez RJ, Jiang Y, Tremblay M, Shao Q, Link AJ, Yang ZJ. LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling. Journal of Chemical Information and Modeling. 63: 522-530. PMID 36594886 DOI: 10.1021/acs.jcim.2c00945  0.751
2022 Jiang Y, Stull SL, Shao Q, Yang ZJ. Convergence in determining enzyme functional descriptors across Kemp eliminase variants. Electronic Structure (Bristol, England). 4. PMID 37425623 DOI: 10.1088/2516-1075/acad51  0.732
2022 Jiang Y, Ran X, Yang ZJ. Data-Driven Enzyme Engineering to Identify Function-Enhancing Enzymes. Protein Engineering, Design & Selection : Peds. PMID 36214500 DOI: 10.1093/protein/gzac009  0.619
2022 Fu B, Nazemi A, Levin BJ, Yang Z, Kulik HJ, Balskus EP. Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer. Journal of the American Chemical Society. 144: 11110-11119. PMID 35704859 DOI: 10.1021/jacs.1c13580  0.61
2022 Yang Z, Hajlasz N, Kulik HJ. Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch. The Journal of Physical Chemistry. B. PMID 35481742 DOI: 10.1021/acs.jpcb.2c00762  0.575
2022 Jiang Y, Yan B, Chen Y, Juarez RJ, Yang ZJ. Molecular Dynamics-Derived Descriptor Informs the Impact of Mutation on the Catalytic Turnover Number in Lactonase Across Substrates. The Journal of Physical Chemistry. B. 126: 2486-2495. PMID 35324218 DOI: 10.1021/acs.jpcb.2c00142  0.659
2022 Zeng Y, Gordiichuk P, Ichihara T, Zhang G, Sandoz-Rosado E, Wetzel ED, Tresback J, Yang J, Kozawa D, Yang Z, Kuehne M, Quien M, Yuan Z, Gong X, He G, et al. Irreversible synthesis of an ultrastrong two-dimensional polymeric material. Nature. 602: 91-95. PMID 35110762 DOI: 10.1038/s41586-021-04296-3  0.54
2022 Shao Q, Jiang Y, Yang ZJ. EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling. Journal of Chemical Information and Modeling. 62: 647-655. PMID 35073075 DOI: 10.1021/acs.jcim.1c01424  0.726
2021 Wang X, Zhang C, Jiang Y, Wang W, Zhou Y, Chen Y, Zhang B, Tan RX, Ge HM, Yang ZJ, Liang Y. 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. PMID 34851644 DOI: 10.1021/jacs.1c10760  0.658
2021 Qin ZX, Tremblay M, Hong X, Yang ZJ. Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path. The Journal of Physical Chemistry Letters. 10713-10719. PMID 34709848 DOI: 10.1021/acs.jpclett.1c03116  0.714
2021 Yan B, Ran X, Jiang Y, Torrence SK, Yuan L, Shao Q, Yang ZJ. Rate-Perturbing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling. The Journal of Physical Chemistry. B. PMID 34524819 DOI: 10.1021/acs.jpcb.1c05901  0.66
2021 Yang Z, Kulik HJ. Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of -4-Hydroxy-l-Proline Dehydratase. The Journal of Physical Chemistry. B. PMID 34236200 DOI: 10.1021/acs.jpcb.1c05320  0.63
2021 Dawson CD, Irwin SM, Backman LRF, Le C, Wang JX, Vennelakanti V, Yang Z, Kulik HJ, Drennan CL, Balskus EP. Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase. Cell Chemical Biology. PMID 33773110 DOI: 10.1016/j.chembiol.2021.03.001  0.76
2020 Ritt CL, Werber JR, Wang M, Yang Z, Zhao Y, Kulik HJ, Elimelech M. Ionization behavior of nanoporous polyamide membranes. Proceedings of the National Academy of Sciences of the United States of America. PMID 33184175 DOI: 10.1073/pnas.2008421117  0.5
2020 Houk KN, Liu F, Yang Z, Seeman JI. 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 Ed. in English). PMID 32662195 DOI: 10.1002/Anie.202001654  0.52
2019 Yang Z, Mehmood R, Wang M, Qi HW, Steeves AH, Kulik HJ. Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation. Reaction Chemistry & Engineering. 4: 298-315. PMID 31572618 DOI: 10.1039/C8RE00213D  0.733
2019 Yang Z, Liu F, Steeves AH, Kulik HJ. Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases. The Journal of Physical Chemistry Letters. 3779-3787. PMID 31244268 DOI: 10.1021/acs.jpclett.9b01555  0.714
2019 Xue XS, Jamieson CS, Garcia-Borràs M, Dong X, Yang Z, Houk KN. An Ambimodal Trispericyclic Transition State and Dynamic Control of Periselectivity. Journal of the American Chemical Society. PMID 30623652 DOI: 10.1021/Jacs.8B12674  0.781
2019 Yang Z, Jamieson CS, Xue X, Garcia-Borràs M, Benton T, Dong X, Liu F, Houk K. Mechanisms and Dynamics of Reactions Involving Entropic Intermediates Trends in Chemistry. 1: 22-34. DOI: 10.1016/j.trechm.2019.01.009  0.747
2018 Popov S, Shao B, Bagdasarian AL, Benton TR, Zou L, Yang Z, Houk KN, Nelson HM. Teaching an old carbocation new tricks: Intermolecular C-H insertion reactions of vinyl cations. Science (New York, N.Y.). 361: 381-387. PMID 30049877 DOI: 10.1126/science.aat5440  0.432
2018 Yang Z, Houk KN. The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van 't Hoff. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 29512895 DOI: 10.1002/chem.201706032  0.448
2018 Guan J, Jia C, Li Y, Liu Z, Wang J, Yang Z, Gu C, Su D, Houk KN, Zhang D, Guo X. Direct single-molecule dynamic detection of chemical reactions. Science Advances. 4: eaar2177. PMID 29487914 DOI: 10.1126/Sciadv.Aar2177  0.412
2018 Yang Z, Dong X, Yu Y, Yu P, Li Y, Jamieson C, Houk KN. Relationships Between Product Ratios in Ambimodal Pericyclic Reactions and Bond Lengths in Transition Structures. Journal of the American Chemical Society. PMID 29419295 DOI: 10.1021/Jacs.7B13562  0.766
2018 Yang Z, Yang S, Yu P, Li Y, Doubleday C, Park J, Patel A, Jeon BS, Russell WK, Liu HW, Russell DH, Houk KN. Influence of water and enzyme SpnF on the dynamics and energetics of the ambimodal [6+4]/[4+2] cycloaddition. Proceedings of the National Academy of Sciences of the United States of America. PMID 29348209 DOI: 10.1073/Pnas.1719368115  0.772
2018 Yu Y, Yang Z, Houk KN. 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. 117: 1360-1366. DOI: 10.1080/00268976.2018.1549338  0.422
2018 Yang Z, Zou L, Yu Y, Liu F, Dong X, Houk K. Molecular dynamics of the two-stage mechanism of cyclopentadiene dimerization: concerted or stepwise? Chemical Physics. 514: 120-125. DOI: 10.1016/j.chemphys.2018.02.020  0.357
2018 Yang Z, Houk KN. Frontispiece: The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van ’t Hoff Chemistry - a European Journal. 24. DOI: 10.1002/chem.201881661  0.386
2017 Noey EL, Yang Z, Li Y, Yu H, Richey RN, Merritt JM, Kjell DP, Houk KN. Correction to Origins of Regioselectivity in the Fischer Indole Synthesis of a Selective Androgen Receptor Modulator. The Journal of Organic Chemistry. PMID 29072838 DOI: 10.1021/Acs.Joc.7B02416  0.708
2017 Liu F, Yang Z, Yu Y, Mei Y, Houk KN. Bimodal Evans-Polanyi Relationships in Dioxirane Oxidations of sp3 C-H: Non-Perfect Synchronization in Generation of Delocalized Radical Intermediates. Journal of the American Chemical Society. PMID 29069541 DOI: 10.1021/Jacs.7B07988  0.379
2017 Ohashi M, Liu F, Hai Y, Chen M, Tang MC, Yang Z, Sato M, Watanabe K, Houk KN, Tang Y. SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis. Nature. PMID 28902839 DOI: 10.1038/Nature23882  0.53
2017 Zhao J, Brosmer JL, Tang Q, Yang Z, Houk KN, Diaconescu PL, Kwon O. Intramolecular Crossed [2 + 2] Photocycloaddition Through Visible Light-Induced Energy Transfer. Journal of the American Chemical Society. PMID 28683547 DOI: 10.1021/Jacs.7B05277  0.365
2017 Grayson MN, Yang Z, Houk KN. Chronology of CH···O Hydrogen Bonding from Molecular Dynamics Studies of the Phosphoric Acid-Catalyzed Allylboration of Benzaldehyde. Journal of the American Chemical Society. PMID 28556660 DOI: 10.1021/jacs.7b03847  0.389
2017 Yu P, Chen TQ, Yang Z, He CQ, Patel A, Lam YH, Liu CY, Houk KN. Mechanisms and Origins of Periselectivity of the Ambimodal [6+4] Cycloadditions of Tropone to Dimethylfulvene. Journal of the American Chemical Society. PMID 28535677 DOI: 10.1021/Jacs.7B02966  0.687
2017 Noey EL, Yang Z, Li Y, Yu H, Richey RN, Merritt JM, Kjell DP, Houk KN. Origins of regioselectivity in the Fischer indole synthesis of a selective androgen receptor modulator. The Journal of Organic Chemistry. PMID 28467062 DOI: 10.1021/Acs.Joc.7B00878  0.769
2017 He T, Ren A, Chen S, Yang Z, Yu P, Chen Y, Ding X, Shen L, Zhang H, Zou L. A theoretical study of phosphorescent Cu(I) complexes with 2-(2'quinolyl)imidazole and POP mixed ligands Organic Electronics. 45: 9-19. DOI: 10.1016/J.Orgel.2017.02.039  0.582
2016 Yu P, Yang Z, Liang Y, Hong X, Li Y, Houk KN. Distortion-Controlled Reactivity and Molecular Dynamics of Dehydro-Diels-Alder Reactions. Journal of the American Chemical Society. PMID 27286801 DOI: 10.1021/Jacs.6B04113  0.698
2016 Liu F, Yang Z, Mei Y, Houk KN. QM/QM' Direct Molecular Dynamics of Water-Accelerated Diels-Alder Reaction. The Journal of Physical Chemistry. B. PMID 27092967 DOI: 10.1021/acs.jpcb.6b02336  0.399
2016 Yang Z, Yu P, Houk KN. Molecular Dynamics of Dimethyldioxirane C-H Oxidation. Journal of the American Chemical Society. PMID 26964643 DOI: 10.1021/Jacs.6B01028  0.68
2016 Patel A, Chen Z, Yang Z, Gutierrez O, Liu HW, Houk KN, Singleton DA. Dynamically complex [6+4] and [4+2] cycloadditions in the biosynthesis of spinosyn A. Journal of the American Chemical Society. PMID 26909570 DOI: 10.1021/Jacs.6B00017  0.526
2015 Yang Z, Doubleday C, Houk KN. QM/MM Protocol for Direct Molecular Dynamics of Chemical Reactions in Solution: The Water-Accelerated Diels-Alder Reaction. Journal of Chemical Theory and Computation. PMID 26588803 DOI: 10.1021/acs.jctc.5b01029  0.438
2015 Hong X, Bercovici DA, Yang Z, Al-Bataineh N, Srinivasan R, Dhakal RC, Houk KN, Brewer M. Mechanism and Dynamics of Intramolecular C-H Insertion Reactions of 1-Aza-2-azoniaallene Salts. Journal of the American Chemical Society. 137: 9100-7. PMID 26151292 DOI: 10.1021/Jacs.5B04474  0.431
2015 Hong X, Bercovici DA, Yang Z, Al-Bataineh N, Srinivasan R, Dhakal RC, Houk KN, Brewer M. Mechanism and Dynamics of Intramolecular C-H Insertion Reactions of 1-Aza-2-azoniaallene Salts Journal of the American Chemical Society. 137: 9100-9107. DOI: 10.1021/jacs.5b04474  0.408
2014 Yang Z, Jiménez-Osés G, López CJ, Bridges MD, Houk KN, Hubbell WL. Long-range distance measurements in proteins at physiological temperatures using saturation recovery EPR spectroscopy. Journal of the American Chemical Society. 136: 15356-65. PMID 25290172 DOI: 10.1021/Ja5083206  0.556
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