Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

Solubilization in Mixed Micelles Studied by Molecular Dynamics Simulations and COSMOmic

(2014) Sandra Storm et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region

(2014) Markéta Paloncýová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Taste of Sugar at the Membrane: Thermodynamics and Kinetics of the Interaction of a Disaccharide with Lipid Bilayers

(2013) Jianhui Tian et al.   BIOPHYSICAL JOURNAL

One-dimensional potential of mean force underestimates activation barrier for transport across flexible lipid membranes

(2013) Dmitry I. Kopelevich   JOURNAL OF CHEMICAL PHYSICS

Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients

(2013) Sven Jakobtorweihen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Free Energetics of Arginine Permeation into Model DMPC Lipid Bilayers: Coupling of Effective Counterion Concentration and Lateral Bilayer Dimensions

(2013) Yuan Hu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Warfarin’s Structural Diversity Influences Its Phospholipid Bilayer Membrane Permeation

(2013) Björn C. G. Karlsson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers

(2013) Markéta Paloncýová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations of Membrane–Sugar Interactions

(2013) Jon Kapla et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Different Interactions of Lysine and Arginine Side Chains with Lipid Membranes

(2013) Libo Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers

(2013) Joakim P. M. Jämbeck et al.   Journal of Physical Chemistry Letters

Binding of Serotonin to Lipid Membranes

(2013) Günther H. Peters et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Prediction of Micelle/Water and Liposome/Water Partition Coefficients Based on Molecular Dynamics Simulations, COSMO-RS, and COSMOmic

(2013) Thomas Ingram et al.   LANGMUIR

Molecular Dynamics Simulation of SDS and CTAB Micellization and Prediction of Partition Equilibria with COSMOmic

(2013) Sandra Storm et al.   LANGMUIR

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers

(2012) Igor Vorobyov et al.   Journal of Chemical Theory and Computation

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer

(2012) Markéta Paloncýová et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

(2012) Thomas J. Piggot et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of the Interactions of DMSO with DPPC and DOPC Phospholipid Membranes

(2012) Zak E. Hughes et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes

(2012) Christian L. Wennberg et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural Effects and Translocation of Doxorubicin in a DPPC/Chol Bilayer: The Role of Cholesterol

(2011) Tyrone J. Yacoub et al.   BIOPHYSICAL JOURNAL

Capacities of Membrane Lipids to Accumulate Neutral Organic Chemicals

(2011) Satoshi Endo et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Thermodynamic study of benzocaine insertion into different lipid bilayers

(2011) J. J. López Cascales et al.   JOURNAL OF CHEMICAL PHYSICS

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers

(2011) Chris Neale et al.   Journal of Chemical Theory and Computation

DRUG DISCOVERY INTERFACE: Functional Group Dependence of Solute Partitioning to Various Locations within a DOPC Bilayer: A Comparison of Molecular Dynamics Simulations with Experiment

(2011) Ravindra W. Tejwani et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

The COSMO and COSMO-RS solvation models

(2011) Andreas Klamt   Wiley Interdisciplinary Reviews-Computational Molecular Science

Partitioning of Nonsteroidal Antiinflammatory Drugs in Lipid Membranes: A Molecular Dynamics Simulation Study

(2010) Mohan Babu Boggara et al.   BIOPHYSICAL JOURNAL

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

(2010) Pär Bjelkmar et al.   Journal of Chemical Theory and Computation

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

(2010) Jochen S. Hub 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

COSMO-RS: An Alternative to Simulation for Calculating Thermodynamic Properties of Liquid Mixtures

(2010) Andreas Klamt et al.   Annual Review of Chemical and Biomolecular Engineering

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Evaluation of Liposome−Water Partitioning for Predicting Bioaccumulation Potential of Hydrophobic Organic Chemicals

(2009) Stephan A. van der Heijden et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The role of lipid composition for insertion and stabilization of amino acids in membranes

(2009) Anna C. V. Johansson et al.   JOURNAL OF CHEMICAL PHYSICS

Properties and Permeability of Hypericin and Brominated Hypericin in Lipid Membranes

(2009) Emma S. E. Eriksson et al.   Journal of Chemical Theory and Computation

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Permeability of Small Molecules through a Lipid Bilayer: A Multiscale Simulation Study

(2009) Mario Orsi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Distribution and Dynamics of Adamantanes in a Lipid Bilayer

(2008) Chee Foong Chew et al.   BIOPHYSICAL JOURNAL

Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations

(2008) Justin L. MacCallum et al.   BIOPHYSICAL JOURNAL

Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer

(2008) Edvin Erdtman et al.   CHEMICAL PHYSICS LETTERS

Toward a Class-Independent Quantitative Structure−Activity Relationship Model for Uncouplers of Oxidative Phosphorylation

(2008) Simon Spycher et al.   CHEMICAL RESEARCH IN TOXICOLOGY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

COSMOmic: A Mechanistic Approach to the Calculation of Membrane−Water Partition Coefficients and Internal Distributions within Membranes and Micelles

(2008) Andreas Klamt et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Influence of Ethanol on Lipid Membranes:  From Lateral Pressure Profiles to Dynamics and Partitioning

(2008) Emma Terama et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY