List of works - Junmei Wang

3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtypes CB1 and CB2. A combined NMR and CoMFA approach

scientific article published in January 2006

A fast and high-quality charge model for the next generation general AMBER force field

scientific article published on 01 September 2020

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

scientific article (publication date: December 2003)

A rule-based algorithm for automatic bond type perception

scientific article published on 31 October 2012

ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules?

scientific article published in March 2007

ADME evaluation in drug discovery. 8. The prediction of human intestinal absorption by a support vector machine

scientific article published on 12 October 2007

ADME evaluation in drug discovery. 9. Prediction of oral bioavailability in humans based on molecular properties and structural fingerprints

scientific article published on 16 May 2011

ADMET evaluation in drug discovery. 11. PharmacoKinetics Knowledge Base (PKKB): a comprehensive database of pharmacokinetic and toxic properties for drugs

scientific article

ADMET evaluation in drug discovery. 12. Development of binary classification models for prediction of hERG potassium channel blockage

scientific article (publication date: 2 April 2012)

Accelerated conformational entropy calculations using graphic processing units

scientific article published in August 2013

Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.

scientific article published on July 2011

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient ⬇️

scientific article published on September 22, 2011

Applications of genetic algorithms on the structure-activity relationship analysis of some cinnamamides

scientific article published in September 1999

Aqueous solubility prediction based on weighted atom type counts and solvent accessible surface areas

scientific article

Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models

scientific article published on 8 July 2013

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

scientific article

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

scientific article published on 14 October 2010

Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search

scientific article published in August 1999

Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3

scientific article published on 14 September 2018

Characterization of flavonoids by aluminum complexation and collisionally activated dissociation

scientific article

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

scientific article published on 07 June 2018

Crystal structure of the human sterol transporter ABCG5/ABCG8.

scientific article published on 04 May 2016

Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent

scientific article published on 27 January 2021

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations ⬇️

scientific article published on April 24, 2012

Development and Evaluation of Geometry Optimization Algorithms in Conjunction with ANI Potentials

scientific article published on 12 January 2022

Development and Testing of Druglike Screening Libraries

scientific article published on 03 January 2019

Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy

scientific article published on 04 February 2019

Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability

scientific article published on 10 March 2011

Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies

scientific article

Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes

scientific article published on 5 July 2012

Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization

scientific article

Development of reliable aqueous solubility models and their application in druglike analysis

scientific article

Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore

scientific article (publication date: June 2016)

Discovery, modeling, and human pharmacokinetics of N-(2-acetyl-4,6-dimethylphenyl)-3-(3,4-dimethylisoxazol-5-ylsulfamoyl)thiophene-2-carboxamide (TBC3711), a second generation, ETA selective, and orally bioavailable endothelin antagonist

scientific article published in April 2004

Drug and drug candidate building block analysis

scientific article

Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines

scientific article published on 27 November 2012

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines

scientific article

Drug-likeness analysis of traditional Chinese medicines: prediction of drug-likeness using machine learning approaches.

scientific article published on 20 September 2012

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16-22 Dimer

scientific article published on 28 January 2019

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of PHF6 Peptide of Tau Protein

scientific article published on 07 September 2021

Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations

scientific article published on 01 September 2020

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

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

scientific article

Fast Approaches for Molecular Polarizability Calculations

scientific article published on 27 April 2007

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

scientific article published on 25 February 2020

GPCR structure-based virtual screening approach for CB2 antagonist search

scientific article

Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion

scientific article published in November 2006

High-resolution crystal structure of the human CB1 cannabinoid receptor

scientific article

How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?

scientific article published on 19 November 2020

Identification of a specific inhibitor of the dishevelled PDZ domain

scientific article published in November 2005

Landscape of drug-resistance mutations in kinase regulatory hotspots

scientific article published on 08 June 2020

MORT: a powerful foundational library for computational biology and CADD.

scientific article published on 27 June 2014

Modeling compound-target interaction network of traditional Chinese medicines for type II diabetes mellitus: insight for polypharmacology and drug design

scientific article published on 26 June 2013

Molecular Mechanism and Kinetics of Amyloid-β42 Aggregate Formation: A Simulation Study

scientific article published on 11 November 2019

Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design

scientific article

Molecular mechanism of ultrasound interaction with a blood brain barrier model

scientific article published on 01 July 2020

New application of in silico methods in identifying mechanisms of action and key components of anti-cancer herbal formulation YIV-906 (PHY906)

scientific article published on 16 October 2019

New-generation amber united-atom force field

scientific article published in July 2006

P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape

scientific article (publication date: July 2014)

Polarization effects in molecular mechanical force fields

scientific article published on 24 July 2009

Prediction of Drug-Drug Interactions Between Opioids and Overdosed Benzodiazepines Using Physiologically Based Pharmacokinetic (PBPK) Modeling and Simulation

scientific article published on 01 September 2019

Prediction of the Binding Affinities and Selectivity for CB1 and CB2 Ligands Using Homology Modeling, Molecular Docking, Molecular Dynamics Simulations, and MM-PBSA Binding Free Energy Calculations

scientific article published on 02 April 2020

Transmembrane Polar Relay Drives the Allosteric Regulation for ABCG5/G8 Sterol Transporter

scientific article published on 19 November 2020

List of works by Junmei Wang

3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtypes CB1 and CB2. A combined NMR and CoMFA approach

A fast and high-quality charge model for the next generation general AMBER force field

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

A rule-based algorithm for automatic bond type perception

ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules?

ADME evaluation in drug discovery. 8. The prediction of human intestinal absorption by a support vector machine

ADME evaluation in drug discovery. 9. Prediction of oral bioavailability in humans based on molecular properties and structural fingerprints

ADMET evaluation in drug discovery. 11. PharmacoKinetics Knowledge Base (PKKB): a comprehensive database of pharmacokinetic and toxic properties for drugs

ADMET evaluation in drug discovery. 12. Development of binary classification models for prediction of hERG potassium channel blockage

Accelerated conformational entropy calculations using graphic processing units

Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.

Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient ⬇️

Applications of genetic algorithms on the structure-activity relationship analysis of some cinnamamides

Aqueous solubility prediction based on weighted atom type counts and solvent accessible surface areas

Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search

Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3

Characterization of flavonoids by aluminum complexation and collisionally activated dissociation

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

Crystal structure of the human sterol transporter ABCG5/ABCG8.

Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations ⬇️

Development and Evaluation of Geometry Optimization Algorithms in Conjunction with ANI Potentials

Development and Testing of Druglike Screening Libraries

Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy

Development of polarizable models for molecular mechanical calculations I: parameterization of atomic polarizability

Development of polarizable models for molecular mechanical calculations II: induced dipole models significantly improve accuracy of intermolecular interaction energies

Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes

Development of polarizable models for molecular mechanical calculations. 4. van der Waals parametrization

Development of reliable aqueous solubility models and their application in druglike analysis

Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore

Discovery, modeling, and human pharmacokinetics of N-(2-acetyl-4,6-dimethylphenyl)-3-(3,4-dimethylisoxazol-5-ylsulfamoyl)thiophene-2-carboxamide (TBC3711), a second generation, ETA selective, and orally bioavailable endothelin antagonist

Drug and drug candidate building block analysis

Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines

Drug-likeness analysis of traditional Chinese medicines: prediction of drug-likeness using machine learning approaches.

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16-22 Dimer

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of PHF6 Peptide of Tau Protein

Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations

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

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

Fast Approaches for Molecular Polarizability Calculations

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

GPCR structure-based virtual screening approach for CB2 antagonist search

Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion

High-resolution crystal structure of the human CB1 cannabinoid receptor

How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?

Identification of a specific inhibitor of the dishevelled PDZ domain

Landscape of drug-resistance mutations in kinase regulatory hotspots

MORT: a powerful foundational library for computational biology and CADD.

Modeling compound-target interaction network of traditional Chinese medicines for type II diabetes mellitus: insight for polypharmacology and drug design

Molecular Mechanism and Kinetics of Amyloid-β42 Aggregate Formation: A Simulation Study

Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design

Molecular mechanism of ultrasound interaction with a blood brain barrier model

New application of in silico methods in identifying mechanisms of action and key components of anti-cancer herbal formulation YIV-906 (PHY906)

New-generation amber united-atom force field

P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape

Polarization effects in molecular mechanical force fields

Prediction of Drug-Drug Interactions Between Opioids and Overdosed Benzodiazepines Using Physiologically Based Pharmacokinetic (PBPK) Modeling and Simulation

Prediction of the Binding Affinities and Selectivity for CB1 and CB2 Ligands Using Homology Modeling, Molecular Docking, Molecular Dynamics Simulations, and MM-PBSA Binding Free Energy Calculations

Transmembrane Polar Relay Drives the Allosteric Regulation for ABCG5/G8 Sterol Transporter