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Theoretical and Computational Chemistry

Working Paper

EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation

Qianzhen Shao, Yaoyukun Jiang, Zhongyue Yang

Version 2 posted 20 June 2023

527

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Theoretical and Computational Chemistry

Working Paper

EnzyKR: A Chirality-Aware Deep Learning Model for Predicting the Outcomes of the Hydrolase-Catalyzed Kinetic Resolution

Xinchun Ran, Yaoyukun Jiang, Qianzhen Shao, Zhongyue J. Yang

Version 2 posted 12 September 2023

425

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Predicting 3D Structures of Lasso Peptides

Xingyu Ouyang, Xinchun Ran, Han Xu, Yi-Lei Zhao, A. James Link, Zhongyue Yang

Version 2 posted 14 October 2024

762

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Physical Chemistry

Review

Physics-based Modeling in the New Era of Enzyme Engineering

Christopher Jurich, Qianzhen Shao, Xinchun Ran, Zhongyue Yang

Version 1 posted 10 September 2024

549

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Theoretical and Computational Chemistry

Working Paper

SubTuner: a Physics-Guided Computational Tool for Modifying Enzymatic Substrate Preference and Its Application to Anion Methyltransferases

Qianzhen Shao, Asher C. Hollenbeak, Yaoyukun Jiang, Xinchun Ran, Brian O. Bachmann, Zhongyue J. Yang

Version 3 posted 21 March 2025

872

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Biological and Medicinal Chemistry

Working Paper

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

Zhongyue Yang, Fang Liu, Adam H. Steeves, Heather Kulik

Version 1 posted 31 May 2019

560

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Catalysis

Working Paper

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

Bailu Yan, Xinchun Ran, Yaoyukun Jiang, Sarah K. Torrence, Li Yuan, Qianzhen Shao, Zhongyue Yang

Version 1 posted 10 May 2021

335

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Biological and Medicinal Chemistry

Working Paper

Investigating the Non-Electrostatic Component of Substrate Positioning Dynamics

Yaoyukun Jiang, Ning Ding, Qianzhen Shao, Sebastian Stull, Zihao Cheng, Zhongyue Yang

Version 3 posted 17 November 2023

546

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1

Citations

Theoretical and Computational Chemistry

Working Paper

EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling

Qianzhen Shao, Yaoyukun Jiang, Zhongyue Yang

Version 1 posted 24 November 2021

511

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Theoretical and Computational Chemistry

Working Paper

Accelerated Entropic Path Sampling Elucidates Entropic Effects in Mediating the Ambimodal Selectivity of NgnD-Catalyzed Diels–Alder Reaction

Wook Shin, Xinchun Ran, Xin Wang, Zhongyue Yang

Version 1 posted 02 December 2022

238

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Refine Search

27 results in Zhongyue Yang in Authors: Zhongyue Yang

EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation

EnzyKR: A Chirality-Aware Deep Learning Model for Predicting the Outcomes of the Hydrolase-Catalyzed Kinetic Resolution

Predicting 3D Structures of Lasso Peptides

Physics-based Modeling in the New Era of Enzyme Engineering

SubTuner: a Physics-Guided Computational Tool for Modifying Enzymatic Substrate Preference and Its Application to Anion Methyltransferases

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

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

Investigating the Non-Electrostatic Component of Substrate Positioning Dynamics

EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling

Accelerated Entropic Path Sampling Elucidates Entropic Effects in Mediating the Ambimodal Selectivity of NgnD-Catalyzed Diels–Alder Reaction

27 results in Authors: Zhongyue Yang