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 |
0.314 |
|
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 |
0.607 |
|
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 |
0.572 |
|
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 |
0.66 |
|
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 |
0.536 |
|
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 |
0.71 |
|
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 |
0.628 |
|
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 |
0.497 |
|
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 |
0.519 |
|
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 |
0.732 |
|
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 |
0.713 |
|
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 |
0.431 |
|
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 |
0.769 |
|
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 |
0.421 |
|
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 |
0.385 |
|
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 |
0.378 |
|
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 |
0.682 |
|
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 |
0.768 |
|
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 |
0.574 |
|
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 |
0.693 |
|
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 |
0.675 |
|
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 |
0.437 |
|
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 |
0.407 |
|
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 |
|
Show low-probability matches. |