List of works - Yinglong Miao

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

scientific article

Accelerated molecular dynamics simulations of protein folding

scientific article published on 12 June 2015

Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor

scientific article published on 06 September 2016

Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics

article

Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process.

scientific article

All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling

scientific article

All-atom multiscaling and new ensembles for dynamical nanoparticles

scientific article published in July 2006

An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

scientific article published on 26 January 2022

Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics

scientific article published on 07 March 2019

Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering

article

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

scientific article published on 21 January 2014

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State

scientific article published on 10 October 2019

G-protein coupled receptors: advances in simulation and drug discovery

scientific article published on 22 June 2016

GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling

scientific article published on 24 February 2022

Gaussian Accelerated Molecular Dynamics in NAMD.

scientific article published on 30 December 2016

Gaussian Accelerated Molecular Dynamics in OpenMM

scientific article published in 2022

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

scientific article (publication date: 11 August 2015)

General trends of dihedral conformational transitions in a globular protein

scientific article published on 21 January 2016

Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor

scientific article published on 10 October 2016

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

scientific article

Investigation of the conformational dynamics of the apo A2A adenosine receptor

scientific article published on 10 April 2015

Ligand Binding Pathways and Conformational Transitions of the HIV Protease

scientific article published on 2 February 2018

Ligand Binding in the Extracellular Vestibule of the Neurotransmitter Transporter Homologue LeuT.

scientific article

Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor

scientific article

Mapping the allosteric sites of the A2A adenosine receptor.

scientific article

Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor.

scientific article

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors

scientific article published on 22 July 2019

Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding

scientific article published on 25 April 2016

Molecular dynamics/order parameter extrapolation for bionanosystem simulations.

scientific article

Molecular mechanism of off-target effects in CRISPR-Cas9

scientific article

Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding

scientific article published on 01 October 2020

Positive allosteric mechanisms of adenosine A<sub>1</sub> receptor-mediated analgesia

scientific article published on 08 September 2021

Protein–Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics

scientific article published on 31 January 2022

Reactive Center Loop Insertion in α-1-Antitrypsin Captured by Accelerated Molecular Dynamics Simulation

scientific article published on 20 December 2016

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation

scientific article published on 12 March 2018

Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies ⬇️

scientific article published on 09 March 2012

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations.

scientific article

Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein

scientific article published on 20 November 2012

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

scientific article published on 05 July 2016

Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation

article

Viral structural transitions: an all-atom multiscale theory

scientific article published in December 2006

List of works by Yinglong Miao

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

Accelerated molecular dynamics simulations of protein folding

Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor

Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics

Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process.

All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling

All-atom multiscaling and new ensembles for dynamical nanoparticles

An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics

Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State

G-protein coupled receptors: advances in simulation and drug discovery

GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling

Gaussian Accelerated Molecular Dynamics in NAMD.

Gaussian Accelerated Molecular Dynamics in OpenMM

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

General trends of dihedral conformational transitions in a globular protein

Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Investigation of the conformational dynamics of the apo A2A adenosine receptor

Ligand Binding Pathways and Conformational Transitions of the HIV Protease

Ligand Binding in the Extracellular Vestibule of the Neurotransmitter Transporter Homologue LeuT.

Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor

Mapping the allosteric sites of the A2A adenosine receptor.

Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor.

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors

Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding

Molecular dynamics/order parameter extrapolation for bionanosystem simulations.

Molecular mechanism of off-target effects in CRISPR-Cas9

Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding

Positive allosteric mechanisms of adenosine A<sub>1</sub> receptor-mediated analgesia

Protein–Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics

Reactive Center Loop Insertion in α-1-Antitrypsin Captured by Accelerated Molecular Dynamics Simulation

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation

Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies ⬇️

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations.

Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation

Viral structural transitions: an all-atom multiscale theory