List of works - Tong Zhu

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 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 quantum mechanical computational method for modeling electrostatic and solvation effects of protein.

scientific article

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

scientific article published on 2 August 2015

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

scientific article published on 12 March 2013

Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases

scientific article

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

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

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

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

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

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

scientific article published on 02 April 2019

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 of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors

scientific article published on 28 December 2016

Donor Engineering for NIR-II Molecular Fluorophores with Enhanced Fluorescent Performance.

scientific article

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

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 mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling

scientific article published in February 2020

Electronic polarization stabilizes tertiary structure prediction of HP-36.

scientific article

Explore the Chemical Space of Linear Alkanes Pyrolysis via Deep Potential Generator

Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method

article

Exploring the Chemical Space of Linear Alkane Pyrolysis via Deep Potential GENerator

scientific article published on 16 December 2020

Formation Mechanism of a Nonterrestrial C6H Radical: An Ab Initio/RRKM Study on the Reaction of Tetracarbon with Acetylene

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

scientific article published on 01 October 2019

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

scientific article published on 08 February 2012

Fragment quantum mechanical calculation of proteins and its applications

scientific article published on 22 May 2014

Growth of Polycyclic Aromatic Hydrocarbon and Soot Inception by in silico Simulation

scientific article published on 4 April 2022

Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations

scientific article published in August 2019

L-4, a Well-Tolerated and Orally Active Inhibitor of Hedgehog Pathway, Exhibited Potent Anti-tumor Effects Against Medulloblastoma and

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

scientific article published on 24 July 2019

Neural Network Based in Silico Simulation of Combustion Reactions

scientific article published on 27 November 2019

New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment

scientific article published on 27 May 2016

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

Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity

scientific article published on 15 October 2016

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

scientific article

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

scientific article

Quasi-classical trajectory study of the reaction O(3P)+HCl→OH+Cl and O(3P)+DCl→OD+Cl: Vector and scalar properties

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

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

scientific article

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

scientific article published on 13 October 2009

Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins ⬇️

scientific article published on 06 July 2021

THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION O(3P) + HCl → OH + Cl FOR THE 3A″ ELECTRONIC STATES

article

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

scientific article published on 18 September 2019

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

scientific article published on 18 May 2022

List of works by Tong Zhu

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

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

A Fragment Quantum Mechanical Method for Metalloproteins

A New Quantum Calibrated Force Field for Zinc-Protein Complex

A quantum mechanical computational method for modeling electrostatic and solvation effects of protein.

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

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

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

Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases

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

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

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

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

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

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

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

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

Development of an effective polarizable bond method for biomolecular simulation.

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

Discovery of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors

Donor Engineering for NIR-II Molecular Fluorophores with Enhanced Fluorescent Performance.

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

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

Effect of mutations on drug resistance of smoothened receptor toward inhibitors probed by molecular modeling

Electronic polarization stabilizes tertiary structure prediction of HP-36.

Explore the Chemical Space of Linear Alkanes Pyrolysis via Deep Potential Generator

Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method

Exploring the Chemical Space of Linear Alkane Pyrolysis via Deep Potential GENerator

Formation Mechanism of a Nonterrestrial C6H Radical: An Ab Initio/RRKM Study on the Reaction of Tetracarbon with Acetylene

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

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

Fragment quantum mechanical calculation of proteins and its applications

Growth of Polycyclic Aromatic Hydrocarbon and Soot Inception by in silico Simulation

Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations

L-4, a Well-Tolerated and Orally Active Inhibitor of Hedgehog Pathway, Exhibited Potent Anti-tumor Effects Against Medulloblastoma and

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

Neural Network Based in Silico Simulation of Combustion Reactions

New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment

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

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

Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

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

Quasi-classical trajectory study of the reaction O(3P)+HCl→OH+Cl and O(3P)+DCl→OD+Cl: Vector and scalar properties

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

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

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

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins ⬇️

THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION O(3P) + HCl → OH + Cl FOR THE 3A″ ELECTRONIC STATES

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

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