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Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

Xiaoliang Pan, junjie yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang, Jingzhi Pu, Ye Mei, Kwangho Nam, Yihan Shao

Version 1 posted 09 June 2021

674

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1

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Biological and Medicinal Chemistry

Working Paper

A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery

Zhixiong Lin, Junjie Zou, Chunwang Peng, Shuai Liu, Zhipeng Li, Xiao Wan, Dong Fang, Jian Yin, Gianpaolo Gobbo, Yongpan Chen, Jian Ma, Shuhao Wen, Peiyu Zhang, Mingjun Yang

Version 1 posted 16 October 2020

1,048

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1

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Theoretical and Computational Chemistry

Working Paper

Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

Junjie Zou, Jian Yin, Lei Fang, Mingjun Yang, Tianyuan Wang, Weikun Wu, Michael A. Bellucci, Peiyu Zhang

Version 4 posted 16 July 2020

3,219

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Theoretical and Computational Chemistry

Working Paper

A Smart Strategy for Photoresponsive Molecules: Utilizing Generative Pre-trained Transformer and TDDFT Calculations in Drug Delivery

Junjie Hu, Peng Wu, Qi Li, Shiyi Wang, Xianglu Xiao, Zhangming Niu, Binju Wang, Guang Yang

Version 1 posted 08 February 2024

318

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Theoretical and Computational Chemistry

Working Paper

Visualization of Electron Density Changes Along Chemical Reaction Pathways

Chance Lander, Vardhan Satalkar, Junjie Yang, Xiaoliang Pan, Zheng Pei, Aayushi Chatterji, Chungen Liu, Kenneth Nicholas, Robert Cichewicz, Zhibo Yang, Yihan Shao

Version 1 posted 10 May 2022

407

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Theoretical and Computational Chemistry

Working Paper

Can We See the Energy Densities? I. Insights from Real-Time Time-Dependent Density Functional Theory Simulations

junjie yang, Zheng Pei, Jingheng Deng, Qin Wu, Yuezhi Mao, Zhibo Yang, bin wang, Christine M. Aikens, Wanzhen Liang, Yihan Shao

Version 1 posted 24 August 2020

352

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1

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Theoretical and Computational Chemistry

Working Paper

On the Entanglement of Chromophore and Solvent Orbitals

Xinwei Ji, Zheng Pei, Kim Ngan Huynh, Junjie Yang, Xiaoliang Pan, Binju Wang, Yuezhi Mao, Yihan Shao

Version 1 posted 08 October 2024

186

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Chemical Engineering and Industrial Chemistry

Working Paper

Fabrication of superhydrophilic membranes for oil-water separation: A life cycle assessment study

Dixit V Bhalani, Qian Zhang, Yi Yang, Suresh Kumar Jewrajka, Junjie Shen

Version 1 posted 13 September 2024

47

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Theoretical and Computational Chemistry

Working Paper

Development and Comprehensive Benchmark of a High Quality AMBER-Consistent Small Molecule Force Field with Broad Chemical Space Coverage for Molecular Modeling and Free Energy Calculation

Bai Xue, Qingyi Yang, Qiaochu Zhang, Xiao Wan, Dong Fang, Xiaolu Lin, Guangxu Sun, Gianpaolo Gobbo, Fenglei Cao, Alan Mathiowetz, Benjamin Burke, Robert Kumpf, Brajesh Rai, Geoffrey Wood, Frank Pickard, Junmei Wang, Peiyu Zhang, Jian Ma, Alan Jiang, Shuhao Wen, Xinjun Hou, Junjie Zou, Mingjun Yang

Version 3 posted 09 November 2023

1,189

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Theoretical and Computational Chemistry

Working Paper

Does Machine Learning Learn the Physics for Pose Ranking of Fragment-Sized Ligands? A Comparison between Machine Learning and Physics-based Methods

xiao wan, Bai Xue, Michael Bellucci, Zhixiong Lin, Mingjun Yang, Junjie Zou

Version 1 posted 24 May 2024

181

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Refine Search

15 results in Junjie Yang in Authors: Junjie Yang

Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery

Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

A Smart Strategy for Photoresponsive Molecules: Utilizing Generative Pre-trained Transformer and TDDFT Calculations in Drug Delivery

Visualization of Electron Density Changes Along Chemical Reaction Pathways

Can We See the Energy Densities? I. Insights from Real-Time Time-Dependent Density Functional Theory Simulations

On the Entanglement of Chromophore and Solvent Orbitals

Fabrication of superhydrophilic membranes for oil-water separation: A life cycle assessment study

Development and Comprehensive Benchmark of a High Quality AMBER-Consistent Small Molecule Force Field with Broad Chemical Space Coverage for Molecular Modeling and Free Energy Calculation

Does Machine Learning Learn the Physics for Pose Ranking of Fragment-Sized Ligands? A Comparison between Machine Learning and Physics-based Methods

15 results in Authors: Junjie Yang