Membrane permeability of small molecules from unbiased molecular dynamics simulations

Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge

(2020) Andreas Krämer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers

(2020) Mahdi Ghorbani et al.   JOURNAL OF CHEMICAL PHYSICS

Committors, first-passage times, fluxes, Markov states, milestones, and all that

(2019) Alexander M. Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics Simulations of Membrane Permeability

(2019) Richard M. Venable et al.   CHEMICAL REVIEWS

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects

(2019) Andreas Krämer et al.   Journal of Chemical Theory and Computation

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules

(2019) Zhi Yue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Permeability of membranes in the liquid ordered and liquid disordered phases

(2019) An Ghysels et al.   Nature Communications

Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants

(2018) Rui Sun et al.   JOURNAL OF CHEMICAL PHYSICS

Free Energy Calculations of Membrane Permeation: Challenges Due to Strong Headgroup–Solute Interactions

(2018) Nihit Pokhrel et al.   Journal of Chemical Theory and Computation

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

(2018) Oriana De Vos et al.   Journal of Chemical Theory and Computation

Calculating Kinetic Rates and Membrane Permeability from Biased Simulation

(2018) Magd Badaoui et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

(2018) Fatima Sajadi et al.   PeerJ

Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability

(2018) Arman Fathizadeh et al.   Journal of Chemical Theory and Computation

Foundations and latest advances in replica exchange transition interface sampling

(2017) Raffaela Cabriolu et al.   JOURNAL OF CHEMICAL PHYSICS

Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles

(2017) Jeffrey Comer et al.   Journal of Chemical Theory and Computation

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

(2017) An Ghysels et al.   Journal of Chemical Theory and Computation

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Permeability across lipid membranes

(2016) Wataru Shinoda   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Molecular simulation of nonfacilitated membrane permeation

(2016) Ernest Awoonor-Williams et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

(2016) Christopher T. Lee et al.   Journal of Chemical Information and Modeling

Generalized Langevin Methods for Calculating Transmembrane Diffusivity

(2016) Kari Gaalswyk et al.   Journal of Chemical Theory and Computation

Transition-Tempered Metadynamics Is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes

(2016) Rui Sun et al.   Journal of Chemical Theory and Computation

Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning

(2016) Alfredo E. Cardenas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Two Relations to Estimate Membrane Permeability Using Milestoning

(2016) Lane W. Votapka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Subdiffusion in Membrane Permeation of Small Molecules

(2016) Christophe Chipot et al.   Scientific Reports

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Mechanical properties of lipid bilayers from molecular dynamics simulation

(2015) Richard M. Venable et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Simulation Study of the Permeability of a Model Lipid Membrane at the Fluid–Solid Phase Transition

(2015) Lewen Yang et al.   LANGMUIR

A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations

(2014) Timothy S. Carpenter et al.   BIOPHYSICAL JOURNAL

Calculation of Lipid-Bilayer Permeabilities Using an Average Force

(2014) Jeffrey Comer et al.   Journal of Chemical Theory and Computation

Microsecond Molecular Dynamics Simulations of Lipid Mixing

(2014) Chunkit Hong et al.   LANGMUIR

Passive Membrane Permeability: Beyond the Standard Solubility-Diffusion Model

(2013) Giulia Parisio et al.   Journal of Chemical Theory and Computation

New faster CHARMM molecular dynamics engine

(2013) Antti-Pekka Hynninen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

(2010) Peter Eastman et al.   Journal of Chemical Theory and Computation

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

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Potentials of Mean Force and Permeabilities for Carbon Dioxide, Ammonia, and Water Flux across a Rhesus Protein Channel and Lipid Membranes

(2010) Jochen S. Hub et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PACKMOL: A package for building initial configurations for molecular dynamics simulations

(2009) L. Martínez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY