EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations

Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows

(2019) Thorsten B. Blum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin

(2019) Timothée Rivel et al.   Scientific Reports

Curvature as a Collective Coordinate in Enhanced Sampling Membrane Simulations

(2019) Benjamin Bouvier   Journal of Chemical Theory and Computation

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

(2019) Giacomo Fiorin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations

(2019) Md. Iqbal Mahmood et al.   Scientific Reports

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

(2019) Semen Yesylevskyy et al.   Scientific Reports

Computing Curvature Sensitivity of Biomolecules in Membranes by Simulated Buckling

(2018) Federico Elías-Wolff et al.   Journal of Chemical Theory and Computation

Bending Lipid Bilayers: A Closed-Form Collective Variable for Effective Free-Energy Landscapes in Quantitative Biology

(2018) Diego Masone et al.   Journal of Chemical Theory and Computation

The influence of curvature on the properties of the plasma membrane. Insights from atomistic molecular dynamics simulations

(2017) Semen O. Yesylevskyy et al.   Scientific Reports

Determining the Lipid Tilt Modulus by Simulating Membrane Buckles

(2016) Xin Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantifying the Relationship between Curvature and Electric Potential in Lipid Bilayers

(2016) Dennis S. Bruhn et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interaction of C60 fullerenes with asymmetric and curved lipid membranes: a molecular dynamics study

(2016) Yevhen K. Cherniavskyi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The endoplasmic reticulum: structure, function and response to cellular signaling

(2015) Dianne S. Schwarz et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Membrane curvature at a glance

(2015) H. T. McMahon et al.   JOURNAL OF CELL SCIENCE

Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python

(2015) Semen O. Yesylevskyy   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mechanically Activated Ion Channels

(2015) Sanjeev S. Ranade et al.   NEURON

Determination of the shape and curvature of nonplanar lipid bilayers that are bent in a single plane in molecular dynamics simulations

(2014) S. O. Yesylevskyy et al.   JOURNAL OF MOLECULAR MODELING

Determination of mean and Gaussian curvatures of highly curved asymmetric lipid bilayers: the case study of the influence of cholesterol on the membrane shape

(2014) S. O. Yesylevskyy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A flexible algorithm for calculating pair interactions on SIMD architectures

(2013) Szilárd Páll et al.   COMPUTER PHYSICS COMMUNICATIONS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Determining the bending modulus of a lipid membrane by simulating buckling

(2013) Patrick Diggins et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

(2013) Hang Yu et al.   PLoS Computational Biology

Determining the Gaussian Curvature Modulus of Lipid Membranes in Simulations

(2012) Mingyang Hu et al.   BIOPHYSICAL JOURNAL

Improved Parameters for the Martini Coarse-Grained Protein Force Field

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

Membrane curvature and its generation by BAR proteins

(2012) Carsten Mim et al.   TRENDS IN BIOCHEMICAL SCIENCES

Anisotropic surface tension of buckled fluid membranes

(2011) Hiroshi Noguchi   PHYSICAL REVIEW E

Martini Coarse-Grained Force Field: Extension to Carbohydrates

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

CHARMM: The biomolecular simulation program

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

Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations

(2009) H. Jelger Risselada et al.   PHYSICAL CHEMISTRY 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

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane lipids: where they are and how they behave

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