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Chemistry

D-Index
82
Citations
24366
World Ranking
3083
National Ranking
1029

Overview

John Z. H. Zhang is affiliated with New York University in the United States. Their research focuses primarily within the broad field of Biochemistry, Genetics and Molecular Biology, with a significant concentration in Molecular Biology. Other notable subfields include Computational Theory and Mathematics, Atomic and Molecular Physics and Optics, Spectroscopy, and Infectious Diseases.

Their work spans several main topics that highlight computational and chemical methodologies in biological systems. These include:

  • Computational Drug Discovery Methods
  • Protein Structure and Dynamics
  • RNA and protein synthesis mechanisms
  • Advanced Chemical Physics Studies
  • Mass Spectrometry Techniques and Applications
  • Spectroscopy and Quantum Chemical Studies
  • DNA and Nucleic Acid Chemistry

Selected recent papers illustrate the scope and output of their research. Key publications include:

  • "An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein-ligand binding affinity" (2020), published in Nanoscale
  • "Developing an effective polarizable bond method for small molecules with application to optimized molecular docking" (2020), published in RSC Advances
  • "Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax" (2021), published in Physical Chemistry Chemical Physics
  • "A method for efficient calculation of thermal stability of proteins upon point mutations" (2020), published in Physical Chemistry Chemical Physics
  • "Cyclopentadienyl radical formation from the reaction of excited nitrogen atoms with benzene: a theoretical study" (2021), published in Physical Chemistry Chemical Physics

Zhang frequently publishes in the following venues:

  • Physical Chemistry Chemical Physics
  • Nanoscale
  • RSC Advances
  • International Journal of Biological Macromolecules
  • Journal of Molecular Liquids

Their collaborative network includes frequent co-authors such as Yalong Cong, Kaifang Huang, Song Luo, Yifei Qi, and Tong Zhu. These collaborations indicate active engagement in multi-author research projects within their fields of study.

Best Publications

  • End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

    Ercheng Wang;Huiyong Sun;Junmei Wang;Zhe Wang

  • Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy

    Da W. Zhang;J. Z. H. Zhang

  • THEORY AND APPLICATION OF QUANTUM MOLECULAR DYNAMICS

    John Zeng Hui Zhang

  • Full‐dimensional time‐dependent treatment for diatom–diatom reactions: The H2+OH reaction

    Dong H. Zhang;John Z. H. Zhang

  • Dynamics of molecules and chemical reactions

    Robert E. Wyatt;John Z. H. Zhang

  • Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

    Lili Duan;Xiao Liu;John Z.H. Zhang

  • Quantum reactive scattering via the S‐matrix version of the Kohn variational principle: Differential and integral cross sections for D+H2 →HD+H

    John Z. H. Zhang;William H. Miller

  • Analysis of internal short-circuit in a lithium ion cell

    Unknown

  • Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

    Huiyong Sun;Lili Duan;Fu Chen;Hui Liu

  • Quantum reactive scattering with a deep well: Time‐dependent calculation for H+O2 reaction and bound state characterization for HO2

    Dong H. Zhang;John Z. H. Zhang

  • Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation.

    Jinzhe Zeng;Liqun Cao;Mingyuan Xu;Tong Zhu;Tong Zhu

  • DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks.

    Huali Cao;Jingxue Wang;Liping He;Yifei Qi;Yifei Qi

  • Quantum scattering via the S‐matrix version of the Kohn variational principle

    John Z.H. Zhang;Shih I. Chu;Shih I. Chu;William H. Miller

  • MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network.

    Xiaolin Pan;Xiaolin Pan;Hao Wang;Hao Wang;Cuiyu Li;John Z. H. Zhang

  • How to observe the elusive resonances in H or D + H2 → H2 or HD + H reactive scattering

    William H. Miller;John Z. H. Zhang

  • Fragment quantum mechanical calculation of proteins and its applications.

    Xiao He;Tong Zhu;Xianwei Wang;Jinfeng Liu

  • Accurate quantum calculation for the benchmark reaction H2+OH→H2O +H in five‐dimensional space: Reaction probabilities for J=0

    Dong H. Zhang;John Z. H. Zhang

  • ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations

    Jinzhe Zeng;Liqun Cao;Chih Hao Chin;Chih Hao Chin;Haisheng Ren

  • Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. Integrase inhibition

    Sylvia Lee-Huang;Philip Lin Huang;Dawei Zhang;Jae Wook Lee

  • Efficiency exceeding 10% for inverted polymer solar cells with a ZnO/ionic liquid combined cathode interfacial layer

    W. Yu;W. Yu;L. Huang;L. Huang;D. Yang;P. Fu;P. Fu

  • Accurate quantum calculations for H2+OH→H2O+H: Reaction probabilities, cross sections, and rate constants

    Dong H. Zhang;John Z. H. Zhang

  • Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin.

    Changge Ji;Ye Mei;John Z.H. Zhang;John Z.H. Zhang

  • Quantum reactive scattering via the S-matrix version of the Kohn variational principle: Integral cross sections For H+H2(ν1=j1=0)→H2(ν2=1, j2= 1, 3) + H in the energy range Etotal = 0.9–1.4 eV

    John Z.H. Zhang;William H. Miller

  • L2 amplitude density method for multichannel inelastic and rearrangement collisions

    John Z. H. Zhang;Donald J. Kouri;Kenneth Haug;David W. Schwenke

Frequent Co-Authors

Xiao He
Xiao He East China Normal University
Dong H. Zhang
Dong H. Zhang Dalian Institute of Chemical Physics
Ke-Li Han
Ke-Li Han Dalian Institute of Chemical Physics
William H. Miller
William H. Miller University of California, Berkeley
Dawei Zhang
Dawei Zhang University of Shanghai for Science and Technology
Donald G. Truhlar
Donald G. Truhlar University of Minnesota
Zlatko Bačić
Zlatko Bačić New York University
Young-Tae Chang
Young-Tae Chang Pohang University of Science and Technology
Yingkai Zhang
Yingkai Zhang New York University
Paul L. Huang
Paul L. Huang Harvard University

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