Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling

MARTINI Coarse-Grained Models of Polyethylene and Polypropylene

(2015) Emanuele Panizon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lipid Membranes as Solvents for Carbon Nanoparticles

(2014) Jonathan Barnoud et al.   PHYSICAL REVIEW LETTERS

Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers

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

Polystyrene Nanoparticles Perturb Lipid Membranes

(2013) Giulia Rossi et al.   Journal of Physical Chemistry Letters

Partitioning and solubility of C60fullerene in lipid membranes

(2013) G Rossi et al.   PHYSICA SCRIPTA

Insight into NSAID-induced membrane alterations, pathogenesis and therapeutics: Characterization of interaction of NSAIDs with phosphatidylcholine

(2012) Lenard M. Lichtenberger et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

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

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

On Atomistic and Coarse-Grained Models for C60 Fullerene

(2012) Luca Monticelli   Journal of Chemical Theory and Computation

Structural Association of Nonsteroidal Anti-Inflammatory Drugs with Lipid Membranes

(2012) Mohan Babu Boggara et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sampling protein motion and solvent effect during ligand binding

(2012) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Permeation through the Cell Membrane of a Boron-Based β-Lactamase Inhibitor

(2011) Manuela Minozzi et al.   PLoS One

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

(2010) Giulia Rossi et al.   Soft Matter

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Martini Coarse-Grained Force Field: Extension to Carbohydrates

(2009) Cesar A. López et al.   Journal of Chemical Theory and Computation

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

(2009) David L. Mobley et al.   Journal of Chemical Theory and Computation

A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics

(2009) Hwankyu Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Biased Molecular Simulations for Free-Energy Mapping:  A Comparison on the KcsA Channel as a Test Case

(2007) Enrico Piccinini et al.   Journal of Chemical Theory and Computation