In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force

Predicting a Drug’s Membrane Permeability: A Computational Model Validated With in Vitro Permeability Assay Data

(2017) Brian J. Bennion et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations

(2017) Daniela Lopes et al.   PROGRESS IN LIPID RESEARCH

Permeability across lipid membranes

(2016) Wataru Shinoda   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Martini straight: Boosting performance using a shorter cutoff and GPUs

(2016) Djurre H. de Jong et al.   COMPUTER PHYSICS COMMUNICATIONS

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition

(2016) Siegfried S. F. Leung et al.   Journal of Chemical Information and Modeling

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

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

Automated Parametrization of the Coarse-Grained Martini Force Field for Small Organic Molecules

(2015) Tristan Bereau et al.   Journal of Chemical Theory and Computation

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

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

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

More than the sum of its parts: Coarse-grained peptide-lipid interactions from a simple cross-parametrization

(2014) Tristan Bereau et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2014) S. Jakobtorweihen et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?

(2012) Robert V. Swift et al.   Chemical Biology & Drug Design

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

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

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

Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces

(2010) Ana Nikolic et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Optimized convergence for multiple histogram analysis

(2009) Tristan Bereau et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations

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

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

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

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

Toward Prediction of Alkane/Water Partition Coefficients

(2008) Anita Toulmin et al.   JOURNAL OF MEDICINAL CHEMISTRY