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List of works by John Z. H. Zhang

A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods

scientific article published on 28 August 2015

A Coupled Ionization-Conformational Equilibrium Is Required To Understand The Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease.

scientific article published on 8 January 2018

A Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions

scientific article published on 14 September 2020

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

scientific article

A Fragment Quantum Mechanical Method for Metalloproteins

scientific article published on 24 January 2019

A New Quantum Calibrated Force Field for Zinc-Protein Complex

scientific article published on 28 February 2013

A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B.

scientific article

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

scientific article

A force consistent method for electrostatic energy calculation in fluctuating charge model

scientific article published on 01 September 2019

A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase--structural and modeling insight into its functions

scientific article

A new algorithm for construction of coarse-grained sites of large biomolecules

scientific article published on 15 December 2015

A new method for direct calculation of total energy of protein

scientific article published on 01 January 2005

A new quantum method for electrostatic solvation energy of protein

scientific article published in September 2006

A numerically stable restrained electrostatic potential charge fitting method ⬇️

scientific article published on December 28, 2012

Ab Initio QM/MM Free Energy Simulations of Peptide Bond Formation in the Ribosome Support an Eight-Membered Ring Reaction Mechanism ⬇️

scientific article published on September 20, 2012

Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water

scientific article published on 06 August 2019

Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis

scientific article published on 5 February 2014

Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants

scientific article published on 27 November 2018

Accurate quantum mechanical reaction probabilities for the reaction O+H2→OH+H

article

Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines

scientific article published in August 2013

Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor

scientific article published on 06 March 2020

An Approach to Computing Solvent Reorganization Energy

scientific article published on 17 September 2020

An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy

scientific article published on 22 June 2017

An Energy Optimization Strategy Based on the Perfect Conformation of Prolyl Endopeptidase for Improving Catalytic Efficiency

scientific article published on 16 April 2020

An efficient approach for ab initio energy calculation of biopolymers

scientific article published in May 2005

An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins

scientific article published on 12 March 2013

An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins

scientific article published in December 2013

Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent

scientific article

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

Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model

scientific article published on 11 March 2013

Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.

scientific article published on 8 May 2018

BAR-based Optimum Adaptive Steered MD for Configurational Sampling

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

scientific article

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification

scientific article published on 4 January 2018

BAR-based optimum adaptive steered MD for configurational sampling

scientific article published on 14 February 2019

Beyond QM/MM: fragment quantum mechanical methods

scientific article published on 01 September 2014

Binding Modes of Small-Molecule Inhibitors to the EED Pocket of PRC2

scientific article published on 16 January 2020

Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies

scientific article published on 14 June 2019

Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes

scientific article published on 14 December 2018

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics

scientific article published on 5 January 2016

Class I phospho-inositide-3-kinases (PI3Ks) isoform-specific inhibition study by the combination of docking and molecular dynamics simulation

scientific article published in January 2010

Combined Theoretical and Experimental Study on High Diastereoselective Chirality Transfer Based on [2.2]Paracyclophane Derivative Chiral Reagent ⬇️

scientific article published on 08 February 2012

Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase

scientific article

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase

scientific article published in April 2010

Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations

Computational Alanine Scanning with Interaction Entropy for Protein-ligand Binding Free Energies

scientific article

Computational Protein Design with Deep Learning Neural Networks

scientific article published on 20 April 2018

Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field

scientific article published in January 2017

Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1

scientific article published on 03 March 2020

Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential

scientific article

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations

scientific article published in September 2014

Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

scientific article published on 01 May 2015

Coupled two-dimensional main-chain torsional potential for protein dynamics II: performance and validation

scientific article published on 5 March 2015

Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes

Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

scientific article published on 02 April 2019

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

scientific article published on 25 February 2019

DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet

scientific article published on 09 March 2020

Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

scientific article published on 30 September 2019

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

scientific article published on August 2008

Development of a New Scoring Function for Virtual Screening: APBScore

scientific article published on 14 October 2020

Development of an effective polarizable bond method for biomolecular simulation.

scientific article

Direct folding simulation of helical proteins using an effective polarizable bond force field

scientific article published in June 2017

Discovery and characterization of novel, potent, and selective cytochrome P450 2J2 inhibitors

scientific article published on 02 October 2012

Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. fusion [corrected] inhibition

scientific article

Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: part II. integrase inhibition

scientific article published on 22 January 2007

Dissociation of heme from gaseous myoglobin ions studied by infrared multiphoton dissociation spectroscopy and Fourier-transform ion cyclotron resonance mass spectrometry

scientific article published on 01 October 2006

Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy

scientific article published on 16 September 2019

Dynamical Stability and Assembly Cooperativity of β-Sheet Amyloid Oligomers – Effect of Polarization ⬇️

scientific article published on November 5, 2012

Dynamical binding of hydrogen-bond surrogate derived Bak helices to antiapoptotic protein Bcl-xL.

scientific article published on March 2009

Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor–CDK2 Association Probed by Interaction Entropy Method

Effect of interprotein polarization on protein–protein binding energy ⬇️

scientific article published on April 12, 2012

Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex

scientific article published on 8 August 2015

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

scientific article published on 01 July 2019

Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations

scientific article published on 03 February 2017

Effect of self-assembly of fullerene nano-particles on lipid membrane

scientific article

Effect of strong electric field on the conformational integrity of insulin

scientific article published on 12 May 2014

Efficient bond function basis set for pi-pi interaction energies

scientific article published in January 2008

Electronic polarization is important in stabilizing the native structures of proteins

scientific article published on 01 December 2009

Electronic polarization stabilizes tertiary structure prediction of HP-36.

scientific article

Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid

scientific article published on 16 August 2018

Electrostatic polarization is critical for the strong binding in streptavidin-biotin system

scientific article published on 30 March 2012

Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding

scientific article published in April 2010

Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy

scientific article published on 27 March 2013

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

scientific article published on 25 June 2019

Energy and electron transfer in beta-alkynyl-linked porphyrin-[60]fullerene dyads

scientific article published on 01 July 2006

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding

scientific article published on 19 March 2020

Erratum to “Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. Integrase inhibition” [Biochem. Biophys. Res. Commun. 354 (2007) 872–878]

scientific article published in May 2007

Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins

scientific article

Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.

scientific article published on 8 July 2016

Exploring the Molecular Mechanism of Stabilization of the Adhesion Domains of Human CD2 by N-Glycosylation ⬇️

scientific article published on September 18, 2012

Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field

article

Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy ⬇️

scientific article published on 02 August 2010

Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds

scientific article published on 01 August 2010

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water

scientific article published on 05 March 2012

Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study

scientific article published on 01 October 2019

Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters

scientific article published on 5 April 2017

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

scientific article published on 08 February 2012

Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins

scientific article published on 21 December 2015

Fragment quantum mechanical calculation of proteins and its applications

scientific article published on 22 May 2014

Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method

scientific article published on 6 March 2017

Fully quantum mechanical energy optimization for protein-ligand structure

scientific article

Functional loop dynamics of the streptavidin-biotin complex

scientific article

Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions.

scientific article published on January 2009

Glycosylation Modulates Human CD2-CD58 Adhesion via Conformational Adjustment

scientific article published on 26 May 2015

How CuCl and CuCl2 Insert into C-N Bonds of Diazo Compounds: An Electronic Structure and Mechanistic Study

scientific article published on 04 March 2020

Hybrid QM/MM study of FMO complex with polarized protein-specific charge

scientific article

Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory.

scientific article published on 4 December 2017

Identification of three new compounds that directly target human serine hydroxymethyltransferase SHMT2

scientific article published on 11 August 2020

Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin.

scientific article

Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization

scientific article published on 20 May 2013

Insights on Na(+) binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM.

scientific article

Interaction Entropy for Computational Alanine Scanning

scientific article published on 13 April 2017

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

scientific article published on 8 April 2016

Interaction entropy for protein-protein binding

scientific article published in March 2017

Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization.

scientific article

L2 amplitude density method for multichannel inelastic and rearrangement collisions

article

Mechanistic Studies of CO2 Cycloaddition Reaction Catalyzed by Amine-Functionalized Ionic Liquids

scientific article published on 10 September 2019

Molecular Dynamics Simulation Study on the Molecular Structures of the Amylin Fibril Models ⬇️

scientific article published on November 26, 2012

Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential

scientific article published on 24 July 2019

Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective

scientific article published on 15 April 2020

Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization

scientific article published on 27 January 2020

Molecular dynamic simulation of the Kv1.2 voltage-gated potassium channel in open and closed state conformations

scientific article published on 01 December 2008

Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers

scientific article published on 14 May 2013

Molecular dynamics simulation of protein crystal with polarized protein-specific force field

scientific article published on 16 October 2014

Molecular dynamics study of DNA binding by INT-DBD under a polarized force field

scientific article published on 05 February 2013

NMR scalar coupling constant reveals that intraprotein hydrogen bonds are dynamically stabilized by electronic polarization

scientific article published in October 2009

Neural Network Based in Silico Simulation of Combustion Reactions

scientific article published on 27 November 2019

New Advance in Computational Chemistry:  Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy

scientific article

Nonadiabatic effects in the H+D2 reaction

article

Nonadiabatic reactant-product decoupling calculation for the F(2P(1/2)) + H2 reaction

scientific article published on 01 April 2006

Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine

scientific article published on 20 September 2014

Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.

scientific article published on 28 July 2017

PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity

scientific article

Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix

scientific article published on 12 December 2011

Predicting mutation-induced Stark shifts in the active site of a protein with a polarized force field

scientific article

Probing the Ion-Specific Effects at the Water/Air Interface and Water-Mediated Ion Pairing in Sodium Halide Solution with Ab initio Molecular Dynamics

article

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

scientific article published in February 2017

Protein's electronic polarization contributes significantly to its catalytic function ⬇️

scientific article published on May 28, 2011

Protein-Ligand Empirical Interaction Components for Virtual Screening

scientific article

Quantifying the Stabilizing Energy of the Intraprotein Hydrogen Bond Due to Local Mutation ⬇️

scientific article published on September 30, 2011

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

scientific article

Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin.

scientific article published on 23 March 2007

Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method

scientific article

Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations

scientific article published in November 2005

Quantum dynamics study of H+NH3-->H2+NH2 reaction

scientific article published on 01 June 2007

Quantum mechanical algebraic variational methods for inelastic and reactive molecular collisions

article

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

scientific article published on November 2015

Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex

scientific article published in January 2004

Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding.

scientific article published on 16 August 2008

Quantum scattering calculation of the O(1D)+HBr reaction

scientific article published on 01 May 2004

Quantum study of HIV-1 protease-bridge water interaction

scientific article published in October 2007

ReacNetGen: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations

ReacNetGenerator: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations

scientific article published on 26 November 2019

Selective Binding of Antiinfluenza Drugs and Their Analogues to ‘Open’ and ‘Closed’ Conformations of H5N1 Neuraminidase ⬇️

scientific article published on October 14, 2010

Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study

scientific article published on 01 January 2008

Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization

scientific article

Single Biosensor for Simultaneous Quantification of Glucose and pH in a Rat Brain of Diabetic Model Using Both Current and Potential Outputs

scientific article

Storage management strategies in large-scale quantum dynamics calculations

article

Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization

scientific article published on 04 August 2011

Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures

scientific article published on 25 April 2017

Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way.

scientific article

Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning

scientific article published on 06 September 2019

Studying the Effect of Site-Specific Hydrophobicity and Polarization on Hydrogen Bond Energy of Protein Using a Polarizable Method

scientific article published on 23 May 2012

Sulfur-substitution-induced base flipping in the DNA duplex

scientific article published on 01 July 2019

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein

scientific article published on 26 October 2016

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.

scientific article published on 2 September 2013

The critical effect of polarization on the dynamical structure of guanine quadruplex DNA.

scientific article published in March 2013

The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy

scientific article published in May 2006

The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction.

scientific article published in November 2018

The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study

scientific article

The investigation of spin-orbit effect for the F((2)P)+HD reaction

scientific article published on 01 April 2004

The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations

scientific article published on June 2016

Theoretical Understanding of the Thermodynamics and Interactions in Transcriptional Regulator TtgR-Ligand Binding

Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

scientific article

Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding

scientific article published on 24 December 2019

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods

Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins

scientific article published on 28 February 2017

Understanding the Molecular Mechanism of Enzyme Dynamics of Ribonuclease A through Protonation/Deprotonation of HIS48 ⬇️

scientific article published on October 13, 2011

Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling

scientific article published on 18 September 2019

Unveiling the gating mechanism of ECF transporter RibU

scientific article

Variational basis-set calculations of accurate quantum mechanical reaction probabilities

article

neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT

scientific article published on 18 May 2022

pH-dependent conformational ensemble and polymorphism of amyloid-β core fragment

scientific article published on 2 July 2013

ℒ2Calculations of accurate quantal-dynamical reactive scattering transition probabilities and their use to test semiclassical applications

article

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