John Z H Zhang (Yifei Qi)

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 19

Top Topics

Respiratory Syndrome Coronavirus

Molecular Dynamics

Top Venues

Journal of chemical information and modeling

Physical chemistry chemical physics : PCCP

Journal of biomolecular structure & dynamics

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

Publications

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)
Xiangying Zhang, Haotian Gao, Haojie Wang, Zhihang Chen, Zhe Zhang, Xinchong Chen, Yan Li, John Z H Zhang, Ren-Xiao Wang
PLANET: A Multi-objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction. Journal of chemical information and modeling (2023)
Yalong Cong, Mengxin Li, Yifei Qi, John Z H Zhang
A fast-slow method to treat solute dynamics in explicit solvent. Physical chemistry chemical physics : PCCP 24 (23) (2022)
Xudong Zhang, Jun Mao, Min Wei, John Z H Zhang, John Zenghui Zhang
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models. Journal of chemical information and modeling 62 (8) (2022)
Min Wei, Xudong Zhang, Xiaolin Pan, Bo Wang, Changge Ji, John Z H Zhang, John Z H Zhang
HobPre: accurate prediction of human oral bioavailability for small molecules. Journal of cheminformatics 14 (1) (2022)
Xiaoyu Zhao, Song Luo, Kaifang Huang, Danyang Xiong, John Z H Zhang, Lili Duan
Targeting mechanism for SARS-CoV-2 in silico: interaction and key groups of TMPRSS2 toward four potential drugs. Nanoscale 13 (45) (2021)
Yao Liu, Yalong Cong, Chuanxi Zhang, Bohuan Fang, Yue Pan, Qiangzi Li, Chun You, Bei Gao, John Z H Zhang, Tong Zhu, Lujia Zhang
Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement. RSC advances 11 (20) (2021)
Wei Wen, Dading Huang, Jingxiao Bao, John Z H Zhang
Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanning. Physical chemistry chemical physics : PCCP 23 (29) (2021)
Zhendong Li, John Z H Zhang
Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13. Physical chemistry chemical physics : PCCP 23 (25) (2021)
Wei Xia, Liping He, Jingxiao Bao, John Z H Zhang, John Z H Zhang
Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation. Journal of biomolecular structure & dynamics (2021)
Ya Gao, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, John Z H Zhang, Jeffery B Klauda, Göran Widmalm, Syma Khalid, Wonpil Im
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. Journal of chemical information and modeling 61 (2) (2021)
Lei Zheng, Yanmei Chen, Jingxiao Bao, Liping He, Suzhen Dong, John Z H Zhang, John Z H Zhang
Discovery of novel inhibitors of SARS-CoV-2 main protease. Journal of biomolecular structure & dynamics (2021)
Junxiao Chen, Na Li, Xingyu Wang, Jianzhong Chen, John Z H Zhang, Tong Zhu
Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations. Physical chemistry chemical physics : PCCP 23 (17) (2021)
Guanfu Duan, Changge Ji, John Z H Zhang
Developing an effective polarizable bond method for small molecules with application to optimized molecular docking. RSC advances 10 (26) (2020)
Bo Wang, Yifei Qi, Ya Gao, John Z H Zhang
A method for efficient calculation of thermal stability of proteins upon point mutations. Physical chemistry chemical physics : PCCP 22 (16) (2020)
John Z H Zhang, John Zenghui Zhang
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet. Journal of chemical information and modeling 60 (3) (2020)
Liping He, Jingxiao Bao, Yunpeng Yang, Suzhen Dong, Lujia Zhang, John Z H Zhang, John Zenghui Zhang
Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning. Journal of chemical information and modeling 59 (9) (2019)
Huali Cao, Jingxue Wang, Liping He, John Z H Zhang, John Zenghui Zhang
DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks. Journal of chemical information and modeling 59 (4) (2019)
Jumin Lee, Dhilon S Patel, Jonas Ståhle, Sang-Jun Park, Nathan R Kern, Seonghoon Kim, Joonseong Lee, Xi Cheng, Miguel A Valvano, Otto Holst, Yuriy A Knirel, John Z H Zhang, Sunhwan Jo, Jeffery B Klauda, Göran Widmalm, Wonpil Im
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. Journal of chemical theory and computation 15 (1) (2018)