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Molecular Dynamics Simulations of Membrane Permeability

Chemical reviews, 2019-05, Vol.119 (9), p.5954-5997

2019

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CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

Biophysical journal, 2014-07, Vol.107 (1), p.134-145

2014

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Mechanical properties of lipid bilayers from molecular dynamics simulation

Chemistry and physics of lipids, 2015-11, Vol.192, p.60-74

2015

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Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

The journal of physical chemistry. B, 2010-06, Vol.114 (23), p.7830-7843

2010

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Permeability of membranes in the liquid ordered and liquid disordered phases

Nature communications, 2019-12, Vol.10 (1), p.5616-12, Article 5616

2019

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Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data

The journal of physical chemistry. B, 2013-09, Vol.117 (35), p.10183-10192

2013

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CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

Journal of chemical theory and computation, 2009-08, Vol.5 (9), p.2353-2370

2009

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Ion-Induced PIP2 Clustering with Martini3: Modification of Phosphate–Ion Interactions and Comparison with CHARMM36

The journal of physical chemistry. B, 2024-03, Vol.128 (9), p.2134-2143

2024

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Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes

Journal of chemical theory and computation, 2017-06, Vol.13 (6), p.2962-2976

2017

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CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

Journal of computational chemistry, 2014-10, Vol.35 (27), p.1997-2004

2014

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Molecular Dynamics Studies of Polyethylene Oxide and Polyethylene Glycol: Hydrodynamic Radius and Shape Anisotropy

Biophysical journal, 2008-08, Vol.95 (4), p.1590-1599

2008

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Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

Journal of chemical theory and computation, 2021-03, Vol.17 (3), p.1562-1580

2021

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Additive empirical force field for hexopyranose monosaccharides

Journal of computational chemistry, 2008-11, Vol.29 (15), p.2543-2564

2008

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Design principles of PI(4,5)P2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy

Proceedings of the National Academy of Sciences - PNAS, 2022-05, Vol.119 (22), p.1-e2202647119

2022

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Membrane permeability of small molecules from unbiased molecular dynamics simulations

The Journal of chemical physics, 2020-09, Vol.153 (12), p.124107

2020

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Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions

The journal of physical chemistry. B, 2017-04, Vol.121 (15), p.3443-3457

2017

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CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids

Journal of chemical theory and computation, 2021-03, Vol.17 (3), p.1581-1595

2021

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Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

Journal of the American Chemical Society, 2014-10, Vol.136 (39), p.13582-13585

2014

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Surface viscosities of lipid bilayers determined from equilibrium molecular dynamics simulations

Biophysical journal, 2023-03, Vol.122 (6), p.1094-1104

2023

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Design principles of PI(4,5)P 2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy

Proceedings of the National Academy of Sciences - PNAS, 2022-05, Vol.119 (22), p.e2202647119

2022

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Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model

Journal of chemical theory and computation, 2018-07, Vol.14 (7), p.3811-3824

2018

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Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions

The journal of physical chemistry. B, 2018-02, Vol.122 (4), p.1484-1494

2018

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Surface viscosities of several lipids determined from equilibrium molecular dynamics simulations

Biophysical journal, 2023-02, Vol.122 (3), p.227a-227a

2023

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Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids

Journal of chemical theory and computation, 2023-05, Vol.19 (9), p.2590-2605

2023

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High-Resolution Structures and Orientations of Antimicrobial Peptides Piscidin 1 and Piscidin 3 in Fluid Bilayers Reveal Tilting, Kinking, and Bilayer Immersion

Journal of the American Chemical Society, 2014-03, Vol.136 (9), p.3491-3504

2014

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Molecular Dynamics Simulations of Membrane Permeability

CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

Mechanical properties of lipid bilayers from molecular dynamics simulation

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Permeability of membranes in the liquid ordered and liquid disordered phases

Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

Ion-Induced PIP2 Clustering with Martini3: Modification of Phosphate–Ion Interactions and Comparison with CHARMM36

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

Molecular Dynamics Studies of Polyethylene Oxide and Polyethylene Glycol: Hydrodynamic Radius and Shape Anisotropy

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

Additive empirical force field for hexopyranose monosaccharides

Design principles of PI(4,5)P2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy

Membrane permeability of small molecules from unbiased molecular dynamics simulations

Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids

Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

Surface viscosities of lipid bilayers determined from equilibrium molecular dynamics simulations

Design principles of PI(4,5)P 2 clustering under protein-free conditions: Specific cation effects and calcium-potassium synergy

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model

Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions

Surface viscosities of several lipids determined from equilibrium molecular dynamics simulations

Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids

High-Resolution Structures and Orientations of Antimicrobial Peptides Piscidin 1 and Piscidin 3 in Fluid Bilayers Reveal Tilting, Kinking, and Bilayer Immersion

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