Jing Huang

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 57

Top Topics

Machine Learning

Crystal Structure

Molecular Dynamics

Top Venues

The journal of physical chemistry. B

Journal of chemical information and modeling

International journal of molecular sciences

This page only lists publications with an associated author ORCID identifier.

Publications

Ye Ding, Jing Huang
Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy. International journal of molecular sciences 25 (3) (2024)
Ye Ding, Jing Huang
Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy. International journal of molecular sciences 25 (3) (2024)
Tengyu Xie, Jing Huang
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? Journal of chemical information and modeling 64 (8) (2024)
Tengyu Xie, Jing Huang
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? Journal of chemical information and modeling (2024)
Ye Ding, Jing Huang
Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy. International journal of molecular sciences 25 (3) (2024)
Lijing Zhang, Xuping Xie, Hannan Luo, Runtong Qian, Yang Yang, Hongtao Yu, Jing Huang, Pei-Yong Shi, Qi Hu
Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell discovery 10 (1) (2024)
Ye Ding, Jing Huang
Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy. International journal of molecular sciences 25 (3) (2024)
Lijing Zhang, Xuping Xie, Hannan Luo, Runtong Qian, Yang Yang, Hongtao Yu, Jing Huang, Pei-Yong Shi, Qi Hu
Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell discovery 10 (1) (2024)
Ye Ding, Jing Huang
DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics. The journal of physical chemistry letters 15 (2) (2024)
Chengqi Zhu, Xiaoli Lu, Tianlong Cai, Kangli Zhu, Lina Shi, Yinjuan Chen, Tianyu Wang, Yaoming Yang, Dandan Tu, Qi Fu, Jing Huang, Ying Zhen
Firefly toxin lucibufagins evolved after the origin of bioluminescence. PNAS nexus 3 (6) (2024)
Lijing Zhang, Xuping Xie, Hannan Luo, Runtong Qian, Yang Yang, Hongtao Yu, Jing Huang, Pei-Yong Shi, Qi Hu
Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell discovery 10 (1) (2024)
Lijing Zhang, Xuping Xie, Hannan Luo, Runtong Qian, Yang Yang, Hongtao Yu, Jing Huang, Pei-Yong Shi, Qi Hu
Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell discovery 10 (1) (2024)
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Matthias Buck, Joshua Buckner, Amedeo Caflisch, Hao-Ting Chang, Xi Cheng, Yeol Kyo Choi, Jhih-Wei Chu, Michael F Crowley, Qiang Cui, Ana Damjanovic, Yuqing Deng, Michael Devereux, Xinqiang Ding, Michael F Feig, Jiali Gao, David R Glowacki, James E Gonzales, Mehdi Bagerhi Hamaneh, Edward D Harder, Ryan L Hayes, Jing Huang, Yandong Huang, Phillip S Hudson, Wonpil Im, Shahidul M Islam, Wei Jiang, Michael R Jones, Silvan Käser, Fiona L Kearns, Nathan R Kern, Jeffery B Klauda, Themis Lazaridis, Jinhyuk Lee, Justin A Lemkul, Xiaorong Liu, Yun Lyna Luo, Alexander D MacKerell, Dan Thomas Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard W Pastor, Amanda R Pittman, Carol Beth Post, Samarjeet Prasad, Jingzhi Pu, John Z H Zhang, Thenmalarchelvi Rathinavelan, Daniel R Roe, Benoı T Roux, Christopher N Rowley, Jana Shen, Andrew C Simmonett, Alexander J Sodt, Kai Töpfer, Meenu Upadhyay, Arjan van der Vaart, Luis Itza Vazquez-Salazar, Richard M Venable, Luke C Warrensford, H Lee Woodcock, Yujin Wu, Charles L Brooks Iii, Bernard R Brooks, Martin Karplus
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The journal of physical chemistry. B (2024)
Tengyu Xie, Jing Huang
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? Journal of chemical information and modeling 64 (8) (2024)
Chengqi Zhu, Xiaoli Lu, Tianlong Cai, Kangli Zhu, Lina Shi, Yinjuan Chen, Tianyu Wang, Yaoming Yang, Dandan Tu, Qi Fu, Jing Huang, Ying Zhen
Firefly toxin lucibufagins evolved after the origin of bioluminescence. PNAS nexus 3 (6) (2024)
Tengyu Xie, Jing Huang
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? Journal of chemical information and modeling 64 (8) (2024)
Ye Ding, Jing Huang
DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics. The journal of physical chemistry letters (2024)
Ye Ding, Jing Huang
DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics. The journal of physical chemistry letters 15 (2) (2024)
Ye Ding, Jing Huang
Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy. International journal of molecular sciences 25 (3) (2024)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Zilin Song, Ye Ding, Jing Huang
Constant advance replicas method for locating minimum energy paths and transition states. Journal of computational chemistry (2023)
Yingnan Hou, Tengyu Xie, Liuqing He, Liang Tao, Jing Huang
Topological links in predicted protein complex structures reveal limitations of AlphaFold. Communications biology 6 (1) (2023)
Wenyi Zhang, Kaiyue Zhang, Jing Huang
A Simple Way to Incorporate Target Structural Information in Molecular Generative Models. Journal of chemical information and modeling (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Ningke Hou, Lei Shuai, Lijing Zhang, Xuping Xie, Kaiming Tang, Yunkai Zhu, Yin Yu, Wenyi Zhang, Qiaozhu Tan, Gongxun Zhong, Zhiyuan Wen, Chong Wang, Xijun He, Hong Huo, Haishan Gao, You Xu, Jing Xue, Chen Peng, Jing Zou, Craig Schindewolf, Vineet Menachery, Wenji Su, Youlang Yuan, Zuyuan Shen, Rong Zhang, Shuo-Feng Yuan, Hongtao Yu, Pei-Yong Shi, Zhigao Bu, Jing Huang, Qi Hu
Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro. ACS central science 9 (2) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B (2023)
Yingnan Hou, Xiaoli Lu, Ziyao Xu, Jiarun Qu, Jing Huang
How a single mutation alters the protein structure: a simulation investigation on protein tyrosine phosphatase SHP2. RSC advances 13 (7) (2023)
Jinfeng Chen, Zongyang Qiu, Jing Huang
Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes. ACS omega 8 (45) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B (2023)
Yingnan Hou, Xiaoli Lu, Ziyao Xu, Jiarun Qu, Jing Huang
How a single mutation alters the protein structure: a simulation investigation on protein tyrosine phosphatase SHP2. RSC advances 13 (7) (2023)
Tianjun Cao, Yu Bai, Paul Buschbeck, Qiaozhu Tan, Michael B Cantrell, Yinjuan Chen, Yanyou Jiang, Run-Zhou Liu, Nana K Ries, Xiaohuo Shi, Yan Sun, Maxwell A Ware, Fenghua Yang, Huan Zhang, Jichang Han, Lihan Zhang, Jing Huang, Martin Lohr, Graham Peers, Xiaobo Li
An unexpected hydratase synthesizes the green light--absorbing pigment fucoxanthin. The Plant cell (2023)
Mengzhun Guo, Kai Zhao, Liang Guo, Rui Zhou, Qiuju He, Kuan Lu, Tian Li, Dandan Liu, Jinfeng Chen, Jing Tang, Xin Fu, Jinyun Zhou, Bei Zheng, Samuel I Mann, Yongdeng Zhang, Jing Huang, Bing Yang, Ting Zhou, Yingjie Lei, Bobo Dang
Copper assisted sequence-specific chemical protein conjugation at a single backbone amide. Nature communications 14 (1) (2023)
Peter Eastman, Raimondas Galvelis, Raul P Pelaez, Charlles R A Abreu, Stephen E Farr, Emilio Gallicchio, Anton Gorenko, Michael M Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A Mitchell, Vijay S Pande, João P G L M Rodrigues, Jaime Rodríguez-Guerra Pedregal, Andrew C Simmonett, Sukrit Singh, Jason Swails, Philip Turner, Yuanqing Wang, Ivy Zhang, John D Chodera, Gianni De Fabritiis, Thomas E Markland
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The journal of physical chemistry. B 128 (1) (2023)
Ningke Hou, Lei Shuai, Lijing Zhang, Xuping Xie, Kaiming Tang, Yunkai Zhu, Yin Yu, Wenyi Zhang, Qiaozhu Tan, Gongxun Zhong, Zhiyuan Wen, Chong Wang, Xijun He, Hong Huo, Haishan Gao, You Xu, Jing Xue, Chen Peng, Jing Zou, Craig Schindewolf, Vineet Menachery, Wenji Su, Youlang Yuan, Zuyuan Shen, Rong Zhang, Shuo-Feng Yuan, Hongtao Yu, Pei-Yong Shi, Zhigao Bu, Jing Huang, Qi Hu
Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro. ACS central science 9 (2) (2023)
Xiaoli Lu, Jing Huang
A thermodynamic investigation of amyloid precursor protein processing by human γ-secretase. Communications biology 5 (1) (2022)
Ruixue Zhang, You Xu, Jun Lan, Shilong Fan, Jing Huang, Fei Xu
Structural Achievability of an NH-π Interaction between Gln and Phe in a Crystal Structure of a Collagen-like Peptide. Biomolecules 12 (10) (2022)
Wenyi Zhang, Jing Huang
EViS: An Enhanced Virtual Screening Approach Based on Pocket-Ligand Similarity. Journal of chemical information and modeling 62 (3) (2022)
Qiaozhu Tan, Ye Ding, Zongyang Qiu, Jing Huang
Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-Hands with the Drude Polarizable Force Field. ACS physical chemistry Au 2 (2) (2021)
Zhijun Pan, Jing Huang, Wei Zhuang
Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study. JACS Au 1 (10) (2021)
François A Thélot, Wenyi Zhang, KangKang Song, Chen Xu, Jing Huang, Maofu Liao
Distinct allosteric mechanisms of first-generation MsbA inhibitors. Science (New York, N.Y.) 374 (6567) (2021)
Qiaozhu Tan, Ye Ding, Zongyang Qiu, Jing Huang
Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-Hands with the Drude Polarizable Force Field. ACS physical chemistry Au 2 (2) (2021)
You Xu, Jing Huang
Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures. Communications chemistry 4 (1) (2021)
Shuai Wang, Zongyang Qiu, Yingnan Hou, Xiya Deng, Wei Xu, Tingting Zheng, Peihan Wu, Shaofang Xie, Weixiang Bian, Chong Zhang, Zewei Sun, Kunpeng Liu, Chao Shan, Aifu Lin, Shibo Jiang, Youhua Xie, Qiang Zhou, Lu Lu, Jing Huang, Xu Li
AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells. Cell research 31 (2) (2021)
Xiaoliang Pan, Junjie Yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang, Jingzhi Pu, Ye Mei, Kwangho Nam, Yihan Shao
Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions. Journal of chemical theory and computation 17 (9) (2021)
You Xu, Jing Huang
Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures. Communications chemistry 4 (1) (2021)
Abhishek A Kognole, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A Lemkul, Jing Huang, Alexander D MacKerell, Wonpil Im
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. Journal of computational chemistry (2021)
Jian Zhu, Jing Huang
Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field. The journal of physical chemistry. B 125 (1) (2020)
Ye Ding, You Xu, Cheng Qian, Jinfeng Chen, Jian Zhu, Houhou Huang, Yi Shi, Jing Huang
Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields. Journal of computer-aided molecular design 34 (4) (2020)
Fang-Yu Lin, Jing Huang, Poonam Pandey, Chetan Rupakheti, Jing Li, Benoı T Roux, Alexander D MacKerell
Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field. Journal of chemical theory and computation 16 (5) (2020)
Renhong Yan, Yaning Li, Yi Shi, Jiayao Zhou, Jianlin Lei, Jing Huang, Qiang Zhou
Cryo-EM structure of the human heteromeric amino acid transporter b0,+AT-rBAT. Science advances 6 (16) (2020)
Ximin Chi, Xueqin Jin, Yun Chen, Xiaoli Lu, Xinyu Tu, Xiaorong Li, Yuanyuan Zhang, Jianlin Lei, Jing Huang, Zhuo Huang, Qiang Zhou, Xiaojing Pan
Structural insights into the gating mechanism of human SLC26A9 mediated by its C-terminal sequence. Cell discovery 6 (2020)
Jing Huang, Andrew C Simmonett, Frank C Pickard, Alexander D MacKerell, Bernard R Brooks
Mapping the Drude polarizable force field onto a multipole and induced dipole model. The Journal of chemical physics 147 (16) (2018)
Gerhard König, Frank C Pickard, Jing Huang, Walter Thiel, Alexander D MacKerell, Bernard R Brooks, Darrin M York
A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules (Basel, Switzerland) 23 (10) (2018)
Mingjun Yang, Jing Huang, Raphael Simon, Lai-Xi Wang, Alexander D MacKerell
Conformational Heterogeneity of the HIV Envelope Glycan Shield. Scientific reports 7 (1) (2017)