Y. Miao

发表

Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor.

J Andrew McCammon, Yinglong Miao, J. Mccammon, 2015, Biophysical journal.

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

J. Mccammon, K. Kappel, Y. Miao, 2015, Quarterly Reviews of Biophysics.

Multi-conformer ensemble docking to difficult protein targets.

Sally R. Ellingson, Jeremy C. Smith, J. Baudry, 2015, The journal of physical chemistry. B.

Activation and dynamic network of the M2 muscarinic receptor

J Andrew McCammon, Yinglong Miao, Sara E Nichols, 2013, Proceedings of the National Academy of Sciences.

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

Jinan Wang, Y. Miao, 2020, The Journal of chemical physics.

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

Jinan Wang, Y. Miao, Yinglong Miao, 2020, bioRxiv.

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

J. Mccammon, Y. Miao, J. McCammon, 2016, Current opinion in structural biology.

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

J. Mccammon, Y. Miao, J. McCammon, 2018, Proceedings of the National Academy of Sciences.

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

J. Baudry, Y. Miao, Yinglong Miao, 2011, Biophysical journal.

Population Based Reweighting of Scaled Molecular Dynamics

J. Mccammon, W. Sinko, C. D. de Oliveira, 2013, The journal of physical chemistry. B.

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

Y. Miao, B. Schiøtt, Heidi Koldsø, 2017, ACS chemical neuroscience.

Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics

Jinan Wang, Y. Miao, A. Bhattarai, 2020, bioRxiv.

Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics.

Y. Miao, Yinglong Miao, 2018, The Journal of chemical physics.

General trends of dihedral conformational transitions in a globular protein

Jeremy C. Smith, J. Mccammon, J. Baudry, 2016, Proteins.

Self-assembly of nanocomponents into composite structures: derivation and simulation of Langevin equations.

Z Shreif, S Pankavich, P Ortoleva, 2009, The Journal of chemical physics.

Mapping of Allosteric Druggable Sites in Activation‐Associated Conformers of the M2 Muscarinic Receptor

Sara E. Nichols, J. Mccammon, Y. Miao, 2014, Chemical biology & drug design.

Mapping the allosteric sites of the A2A adenosine receptor

J. Mccammon, Y. Miao, A. D. Caliman, 2018, Chemical biology & drug design.

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

D. Kozakov, Jinan Wang, Andrey Alekseenko, 2019, bioRxiv.

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

Jinan Wang, Y. Miao, A. Bhattarai, 2019, bioRxiv.

Recent advances in computational studies of GPCR-G protein interactions.

Jinan Wang, Y. Miao, Yinglong Miao, 2019, Advances in protein chemistry and structural biology.

Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications.

J. Mccammon, Y. Miao, J. McCammon, 2017, Annual reports in computational chemistry.

Mechanisms of γ-Secretase Activation and Substrate Processing

M. Wolfe, Y. Miao, A. Bhattarai, 2020, ACS central science.

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors.

Jinan Wang, Y. Miao, 2019, The journal of physical chemistry. B.

Gaussian accelerated molecular dynamics for elucidation of drug pathways

Y. Miao, A. Bhattarai, Yinglong Miao, 2018, Expert opinion on drug discovery.

Ligand Binding Pathways and Conformational Transitions of the HIV Protease.

Chia-en A. Chang, J. Mccammon, Yu‐ming M. Huang, 2018, Biochemistry.

Derivation of mean-square displacements for protein dynamics from elastic incoherent neutron scattering.

Jeremy C. Smith, J. Baudry, Y. Miao, 2012, The journal of physical chemistry. B.

Agonist Binding and G Protein Coupling in Histamine H2 Receptor: A Molecular Dynamics Study

Christian A. Söldner, H. Sticht, Y. Miao, 2020, International journal of molecular sciences.

Quasielastic neutron scattering in biology: Theory and applications.

Jeremy C. Smith, B. Lindner, L. Hong, 2017, Biochimica et biophysica acta. General subjects.

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

Sara E. Nichols, J. Mccammon, Y. Miao, 2014, Physical chemistry chemical physics : PCCP.

Gaussian Accelerated Molecular Dynamics in NAMD

J. Mccammon, Y. Miao, Yui Tik Pang, 2016, Journal of chemical theory and computation.

VirusX: Simulation of Viral Conformational Changes

Y. Miao, 2004 .

Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation.

Jeremy C. Smith, J. Baudry, Y. Miao, 2012, Biophysical journal.

All-atom multiscale computational modeling of viral dynamics

Y. Miao, 2009 .

Mechanism of ligand recognition by human ACE2 receptor

Y. Miao, A. Bhattarai, Shristi Pawnikar, 2020, bioRxiv.

Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor

A. T. Nguyen, A. Christopoulos, L. May, 2018, Scientific Reports.

Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movements

J. Mccammon, W. Rappel, J. Schroeder, 2018, Proceedings of the National Academy of Sciences.

Hybrid finite element and Brownian dynamics method for charged particles.

J. Mccammon, G. Huber, Shenggao Zhou, 2016, The Journal of chemical physics.

Mechanism of Ligand Recognition by Human ACE2 Receptor

Y. Miao, A. Bhattarai, Shristi Pawnikar, 2021, The journal of physical chemistry letters.

Challenges and frontiers of computational modelling of biomolecular recognition

Jinan Wang, Y. Miao, A. Bhattarai, 2022, QRB Discovery.

Pathway and mechanism of drug binding to chemokine receptors revealed by accelerated molecular simulations.

Y. Miao, Shristi Pawnikar, Shristi P. Pawnikar, 2020, Future medicinal chemistry.

AABC_A_247950 1..19

Jinan Wang, Y. Miao, A. Bhattarai, 2022 .

Structures of β1-adrenergic receptor in complex with Gs and ligands of different efficacies

Wei Liu, Jinan Wang, N. Paknejad, 2022, Nature Communications.

Mechanism of tethered agonist-mediated signaling by polycystin-1.

B. Magenheimer, R. Maser, Y. Miao, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Self-assembly of nanocomponents into composite structures: derivation and simulation of Langevin equations.

P. Ortoleva, Y. Miao, S. Pankavich, 2009, The Journal of chemical physics.

Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA.

Y. Miao, B. Liang, Shristi Pawnikar, 2020, Structure.

Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics

P. Sexton, A. Christopoulos, A. Tobin, 2023, eLife.

Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor

Jinan Wang, Y. Miao, A. Bhattarai, 2020, bioRxiv.

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

J. Andrew McCammon, Arthur Christopoulos, Patrick M. Sexton, 2016, Proceedings of the National Academy of Sciences.

Docking simulation and antibiotic discovery targeting the MlaC protein in Gram‐negative bacteria

V. Nizet, J. Mccammon, Yu‐ming M. Huang, 2019, Chemical biology & drug design.

Gaussian Accelerated Molecular Dynamics in OpenMM.

Rommie E. Amaro, Lane W. Votapka, Matthew M Copeland, 2022, The journal of physical chemistry. B.

Predicting Biomolecular Binding Kinetics: A Review.

Jinan Wang, Y. Miao, Hung N. Do, 2022, Journal of chemical theory and computation.

Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

Jeremy C. Smith, L. Hong, Y. Miao, 2013, The European physical journal. E, Soft matter.

Ligand Gaussian accelerated molecular dynamics 2 (LiGaMD2): Improved calculations of ligand binding thermodynamics and kinetics with closed protein pocket

Jinan Wang, Y. Miao, Yinglong Miao, 2022, bioRxiv.

Small Molecules Targeting the RNA-Binding Protein HuR Inhibit Tumor Growth in Xenografts.

Fei Gao, Jinan Wang, Y. Miao, 2023, Journal of medicinal chemistry.

Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives

Jinan Wang, Y. Miao, A. Bhattarai, 2022, Advances and applications in bioinformatics and chemistry : AABC.

Mechanism of RNA recognition by a Musashi RNA-binding protein

Jinan Wang, Y. Miao, Lan Lan, 2020, bioRxiv.

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

J. Andrew McCammon, Jennifer A. Doudna, Giulia Palermo, 2019, ACS central science.

Molecular mechanism of off-target effects in CRISPR-Cas9

Clarisse G. Ricci, J. Mccammon, J. Doudna, 2018, bioRxiv.

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

J Andrew McCammon, Giulia Palermo, Yinglong Miao, 2017, Proceedings of the National Academy of Sciences.

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

J. Andrew McCammon, Giulia Palermo, Ross C. Walker, 2016, ACS central science.

A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif

P. Schmieder, J. Mccammon, E. Krause, 2018, mSphere.

Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein.

Jeremy C. Smith, J. Baudry, L. Hong, 2012, Journal of the American Chemical Society.

Gaussian accelerated molecular dynamics: Principles and applications

Jinan Wang, P. Arantes, G. Palermo, 2021, Wiley interdisciplinary reviews. Computational molecular science.

Molecular Simulations and Drug Discovery of Adenosine Receptors

Jinan Wang, Y. Miao, A. Bhattarai, 2022, Molecules.

G‐Protein‐Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

Yinglong Miao, Apurba Bhattarai, Jinan Wang, 2020, J. Comput. Chem..

Structure and mechanism of the γ-secretase intramembrane protease complex.

M. Wolfe, Y. Miao, Yinglong Miao, 2022, Current opinion in structural biology.

Viral structural transitions: an all-atom multiscale theory.

Yinglong Miao, P. Ortoleva, Y. Miao, 2006, The Journal of chemical physics.

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

J. Andrew McCammon, Victoria A. Feher, Yinglong Miao, 2015, Journal of chemical theory and computation.

Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor

Y. Miao, Hung N. Do, Sana Akhter, 2021, Frontiers in Molecular Biosciences.

Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA.

Y. Miao, B. Liang, Shristi Pawnikar, 2020, Structure.

Recognition of single-stranded nucleic acids by small-molecule splicing modulators

Jinan Wang, M. Reibarkh, J. Douglas, 2021, Nucleic acids research.

Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia

A. T. Nguyen, P. White, P. Sexton, 2021, Nature.

Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction

J. Karanicolas, Jinan Wang, K. Neufeld, 2020, Cancers.

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

William Sinko, Levi C. T. Pierce, J. Andrew McCammon, 2014, Journal of chemical theory and computation.

Ensemble Docking in Drug Discovery.

Rommie E. Amaro, J Andrew McCammon, Rommie E Amaro, 2018, Biophysical journal.

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

V. Nizet, J. Mccammon, Yu‐ming M. Huang, 2016, Protein science : a publication of the Protein Society.

Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

Jeremy C. Smith, L. Hong, Y. Miao, 2013, The European Physical Journal E.

Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.

Yinglong Miao, Abhishek Singharoy, P. Ortoleva, 2012, The journal of physical chemistry. B.

Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods.

A Singharoy, H Joshi, S Cheluvaraja, 2012, Methods in molecular biology.

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

John E. Johnson, Yinglong Miao, P. Ortoleva, 2010, The journal of physical chemistry. B.

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

P. Ortoleva, Y. Miao, 2010, Biopolymers.

Molecular dynamics/order parameter extrapolation for bionanosystem simulations

Yinglong Miao, Peter J. Ortoleva, P. Ortoleva, 2009, J. Comput. Chem..

Mechanism of tethered agonist-mediated signaling by polycystin-1

B. Magenheimer, R. Maser, Y. Miao, 2021, bioRxiv.

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

J. Andrew McCammon, Yinglong Miao, J. Mccammon, 2016, Molecular simulation.

Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein

M. Wolfe, Y. Miao, A. Bhattarai, 2023, Communications Biology.

Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase.

M. Wolfe, Jinan Wang, Y. Miao, 2022, Journal of the American Chemical Society.

Mechanism of Tripeptide Trimming by γ-Secretase

M. Wolfe, Jinan Wang, Y. Miao, 2021, bioRxiv.

Mechanisms of γ-Secretase Activation and Substrate Processing

M. Wolfe, Y. Miao, A. Bhattarai, 2020, bioRxiv.

Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

Jinan Wang, Y. Miao, Hung N. Do, 2023, bioRxiv.

Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

Jinan Wang, Y. Miao, Hung N. Do, 2023, Research square.

Accelerated molecular dynamics simulations of protein folding

Yinglong Miao, Ferran Feixas, Changsun Eun, 2015, J. Comput. Chem..

Computer-aided GPCR drug discovery

Yinglong Miao, Jinan Wang, Apurba Bhattarai, 2020 .

Specific Engineered G Protein Coupling to Histamine Receptors Revealed from Cellular Assay Experiments and Accelerated Molecular Dynamics Simulations

Christian A. Söldner, A. Strasser, Jinan Wang, 2021, International journal of molecular sciences.

Unique Features of Different Classes of G-Protein-Coupled Receptors Revealed from Sequence Coevolutionary and Structural Analysis

R. Levy, A. Haldane, Y. Miao, 2021, bioRxiv.

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

J. Andrew McCammon, Yinglong Miao, J. Mccammon, 2016, Proceedings of the National Academy of Sciences.

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

Jinan Wang, Y. Miao, 2022, Journal of chemical theory and computation.

Protein-protein interaction-Gaussian accelerated molecular dynamics (PPI-GaMD): Characterization of protein binding thermodynamics and kinetics

Jinan Wang, Y. Miao, Yinglong Miao, 2021, bioRxiv.

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

D. Kozakov, Jinan Wang, Andrey Alekseenko, 2019, Frontiers in molecular biosciences.

Investigation of the conformational dynamics of the apo A2A adenosine receptor

J. Mccammon, Y. Miao, Yi Wang, 2015, Protein science : a publication of the Protein Society.

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

J. Enghild, N. Nielsen, Y. Miao, 2017, Biochemistry.

Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations

Y. Miao, B. Liang, D. Cao, 2021, STAR protocols.

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors Revealed by Accelerated Molecular Simulations

Jinan Wang, Y. Miao, Yinglong Miao, 2019, bioRxiv.

Stochastic dynamics of bionanosystems: Multiscale analysis and specialized ensembles.

S Pankavich, Y Miao, J Ortoleva, 2008, The Journal of chemical physics.

All-atom multiscaling and new ensembles for dynamical nanoparticles.

Peter Ortoleva, Yinglong Miao, P. Ortoleva, 2006, The Journal of chemical physics.

Structural basis of agonist specificity of α1A-adrenergic receptor

Jinan Wang, Xin-Yun Huang, Y. Miao, 2023, Nature communications.

Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning

Weiliang Zhu, Chia-En Chang, Y. Miao, 2023, Frontiers in Molecular Biosciences.

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

Jinan Wang, Y. Miao, A. Bhattarai, 2022, Journal of chemical theory and computation.

Activation mechanisms of the first sphingosine‐1‐phosphate receptor

Y. Miao, Alisha D Caliman, J. McCammon, 2017, Protein science : a publication of the Protein Society.