Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers

Prosecco: polarization reintroduced by optimal scaling of electronic continuum correction origin in MD simulations

(2022) Ricky Nencini et al.   BIOPHYSICAL JOURNAL

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

(2021) Semen Yesylevskyy et al.   Journal of Chemical Theory and Computation

Calcium Ion Binding at the Lipid–Water Interface Alters the Ion Permeability of Phospholipid Bilayers

(2021) Evelyne Deplazes et al.   LANGMUIR

The Ca2+ permeation mechanism of the ryanodine receptor revealed by a multi-site ion model

(2020) Aihua Zhang et al.   Nature Communications

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

(2020) E. Duboué-Dijon et al.   JOURNAL OF CHEMICAL PHYSICS

MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes

(2019) Harsh Bhatia et al.   Journal of Chemical Theory and Computation

Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections

(2019) D. A. Tolmachev et al.   Journal of Chemical Theory and Computation

Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations

(2018) Elise Duboué-Dijon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization

(2018) Josef Melcr et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions

(2018) Kyungreem Han et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How well do force fields capture the strength of salt bridges in proteins?

(2018) Mustapha Carab Ahmed et al.   PeerJ

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

(2016) Seonghoon Kim et al.   BIOPHYSICAL JOURNAL

CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field

(2016) Jumin Lee et al.   BIOPHYSICAL JOURNAL

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

(2016) Jejoong Yoo et al.   BIOPOLYMERS

The complex nature of calcium cation interactions with phospholipid bilayers

(2016) Adéla Melcrová et al.   Scientific Reports

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

Understanding Nucleic Acid–Ion Interactions

(2014) Jan Lipfert et al.   Annual Review of Biochemistry

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

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

(2014) Karl T. Debiec et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization

(2014) Miriam Kohagen et al.   Journal of Physical Chemistry Letters

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

Multisite Ion Models That Improve Coordination and Free Energy Calculations in Molecular Dynamics Simulations

(2013) Akansha Saxena et al.   Journal of Chemical Theory and Computation

Ca2+ channel nanodomains boost local Ca2+ amplitude

(2013) M. R. Tadross et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics simulation of cation–phospholipid clustering in phospholipid bilayers: Possible role in stalk formation during membrane fusion

(2012) Hui-Hsu Gavin Tsai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Pteros: Fast and easy to use open-source C++ library for molecular analysis

(2012) Semen O. Yesylevskyy   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ca2+ regulates T-cell receptor activation by modulating the charge property of lipids

(2012) Xiaoshan Shi et al.   NATURE

Membrane curvature and its generation by BAR proteins

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

Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers

(2011) John M. Boettcher et al.   BIOCHEMISTRY

Anisotropic surface tension of buckled fluid membranes

(2011) Hiroshi Noguchi   PHYSICAL REVIEW E

Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules

(2010) I. V. Leontyev 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

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

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

Membrane recognition by phospholipid-binding domains

(2008) Mark A. Lemmon   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanisms of membrane fusion: disparate players and common principles

(2008) Sascha Martens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Membrane lipids: where they are and how they behave

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