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

Molecular Mechanism of Conductance Enhancement in Narrow Cation-Selective Membrane Channels

(2018) Williams E. Miranda et al.   Journal of Physical Chemistry Letters

Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

(2018) Wojciech Kopec et al.   Nature Chemistry

Ion Permeation Mechanism in Epithelial Calcium Channel TRVP6

(2018) Serzhan Sakipov et al.   Scientific Reports

In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways

(2018) Leonard P. Heinz et al.   Scientific Reports

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Ion channels and ion selectivity

(2017) Benoît Roux   Essays in Biochemistry

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Structural Basis for Gating and Activation of RyR1

(2016) Amédée des Georges et al.   CELL

Crystal structure of the epithelial calcium channel TRPV6

(2016) Kei Saotome et al.   NATURE

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Permeation and Dynamics of an Open-Activated TRPV1 Channel

(2015) Leonardo Darré et al.   JOURNAL OF MOLECULAR BIOLOGY

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

(2015) Hui Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of the voltage-gated calcium channel Cav1.1 complex

(2015) J. Wu et al.   SCIENCE

Selecting Ions by Size in a Calcium Channel: The Ryanodine Receptor Case Study

(2014) Dirk Gillespie et al.   BIOPHYSICAL JOURNAL

Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions

(2014) Miriam Kohagen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

(2014) Fernanda Duarte 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

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution

(2014) Zhen Yan et al.   NATURE

Ion permeation in K+ channels occurs by direct Coulomb knock-on

(2014) D. A. Kopfer et al.   SCIENCE

Force fields for divalent cations based on single-ion and ion-pair properties

(2013) Shavkat Mamatkulov et al.   JOURNAL OF 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

Structural basis for Ca2+ selectivity of a voltage-gated calcium channel

(2013) Lin Tang et al.   NATURE

Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

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

Catalysis of Na+ permeation in the bacterial sodium channel NaVAb

(2013) N. Chakrabarti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Modeling and Simulation of Ion Channels

(2012) Christopher Maffeo et al.   CHEMICAL REVIEWS

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Mechanism of Ion Permeation and Selectivity in a Voltage Gated Sodium Channel

(2011) Ben Corry et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Atypical mechanism of conduction in potassium channels

(2009) S. Furini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistically optimal analysis of samples from multiple equilibrium states

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

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

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