List of works - Ye Mei

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

scientific article

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

Accelerated Computation of Free Energy Profile at <i>Ab Initio</i> Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM

scientific article published on 18 February 2021

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

scientific article published on 18 October 2018

Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching

scientific article published on 11 September 2019

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

scientific article published on 5 February 2014

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

scientific article published on 12 January 2017

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 published on February 10, 2013

Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes

scientific article published on 25 November 2019

Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development

scientific article published on 19 February 2019

Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores

scientific article published on 26 December 2019

Bimodal Evans-Polanyi Relationships in Dioxirane Oxidations of sp3 C-H: Non-perfect Synchronization in Generation of Delocalized Radical Intermediates.

scientific article published on 25 October 2017

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

scientific article published on 5 January 2016

Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants ⬇️

scientific article published on May 7, 2011

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

scientific article published on 23 November 2015

Computational Insights into Endo/Exo Selectivity of the Diels-Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level

scientific article published on 11 June 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

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

scientific article published on 02 October 2012

Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1

scientific article published on 13 June 2019

Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

scientific article published on 28 September 2018

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

scientific article published on 21 September 2017

Efficient bond function basis set for pi-pi interaction energies

scientific article published in January 2008

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

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

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

scientific article published on 01 August 2010

Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

scientific article published on 13 March 2019

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

scientific article

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

scientific article

Influence of the Protein Environment on the Electronic Excitation of Chromophores in the Phycoerythrin 545 Light-Harvesting Complex: A Combined MD-QM/MM Method with Polarized Protein-Specific Charge Scheme

scientific article published on 21 February 2019

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions

scientific article published on 01 September 2021

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

scientific article published on 16 October 2014

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

scientific article published on 30 October 2014

New method for direct linear-scaling calculation of electron density of proteins

scientific article published on 01 January 2005

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

scientific article published on 18 May 2015

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

scientific article published on 12 December 2011

Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations

scientific article published on 08 November 2018

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

scientific article

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

scientific article published on 23 March 2007

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

scientific article published in November 2005

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

scientific article published on 16 August 2008

Quantum study of mutational effect in binding of efavirenz to HIV-1 RT.

scientific article published in May 2005

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein

scientific article

Reproducing the low-temperature excitation energy transfer dynamics of phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian

scientific article published on 01 April 2020

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

scientific article

Some practical approaches to treating electrostatic polarization of proteins.

scientific article

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

scientific article published on 04 August 2011

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

scientific article published on 2 September 2013

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

List of works by Ye Mei

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

A new quantum method for electrostatic solvation energy of protein

A numerically stable restrained electrostatic potential charge fitting method ⬇️

Accelerated Computation of Free Energy Profile at <i>Ab Initio</i> Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation

Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching

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

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

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

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

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

Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes

Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development

Benchmarking the Performance of Time-Dependent Density Functional Theory Methods on Biochromophores

Bimodal Evans-Polanyi Relationships in Dioxirane Oxidations of sp3 C-H: Non-perfect Synchronization in Generation of Delocalized Radical Intermediates.

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

Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants ⬇️

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method

Computational Insights into Endo/Exo Selectivity of the Diels-Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level

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

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

Discovery of SBF1 as an allosteric inhibitor targeting the PIF-pocket of 3-phosphoinositide-dependent protein kinase-1

Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

Efficient bond function basis set for pi-pi interaction energies

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

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

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

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

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

Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

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

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

Influence of the Protein Environment on the Electronic Excitation of Chromophores in the Phycoerythrin 545 Light-Harvesting Complex: A Combined MD-QM/MM Method with Polarized Protein-Specific Charge Scheme

Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions

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

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

New method for direct linear-scaling calculation of electron density of proteins

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions

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

Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

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

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

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

Quantum study of mutational effect in binding of efavirenz to HIV-1 RT.

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein

Reproducing the low-temperature excitation energy transfer dynamics of phycoerythrin 545 light-harvesting complex with a structure-based model Hamiltonian

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

Some practical approaches to treating electrostatic polarization of proteins.

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

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

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