Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels

Steady-State Electrodiffusion from the Nernst–Planck Equation Coupled to Local Equilibrium Monte Carlo Simulations

(2012) Dezső Boda et al.   Journal of Chemical Theory and Computation

Mass action in ionic solutions

(2011) Bob Eisenberg   CHEMICAL PHYSICS LETTERS

A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary

(2011) Dezső Boda et al.   JOURNAL OF CHEMICAL PHYSICS

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores

(2011) Kyu Il Lee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Second-order Poisson–Nernst–Planck solver for ion transport

(2011) Qiong Zheng et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Testing the Applicability of Nernst-Planck Theory in Ion Channels: Comparisons with Brownian Dynamics Simulations

(2011) Chen Song et al.   PLoS One

Ion Conduction in Ligand-Gated Ion Channels: Brownian Dynamics Studies of Four Recent Crystal Structures

(2010) Chen Song et al.   BIOPHYSICAL JOURNAL

Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

(2010) Bob Eisenberg et al.   JOURNAL OF CHEMICAL PHYSICS

An efficient algorithm for classical density functional theory in three dimensions: Ionic solutions

(2010) Matthew G. Knepley et al.   JOURNAL OF CHEMICAL PHYSICS

Voltage-dependent inactivation gating at the selectivity filter of the MthK K+channel

(2010) Andrew S. Thomson et al.   JOURNAL OF GENERAL PHYSIOLOGY

Soft Wall Ion Channel in Continuum Representation with Application to Modeling Ion Currents in α-Hemolysin

(2010) Nikolay A. Simakov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural mechanism of C-type inactivation in K+ channels

(2010) Luis G. Cuello et al.   NATURE

Structural basis for the coupling between activation and inactivation gates in K+ channels

(2010) Luis G. Cuello et al.   NATURE

Novel insights into K+ selectivity from high-resolution structures of an open K+ channel pore

(2010) Sheng Ye et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolution of the Human Ion Channel Set

(2009) Surendra Nayak et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

CHARMM: The biomolecular simulation program

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

Model-Based Prediction of the α-Hemolysin Structure in the Hexameric State

(2008) Simone Furini et al.   BIOPHYSICAL JOURNAL

Ion flux through membrane channels-An enhanced algorithm for the Poisson-Nernst-Planck model

(2008) Witold Dyrka et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

(2008) Nicolas Bocquet et al.   NATURE

X-ray structure of a prokaryotic pentameric ligand-gated ion channel

(2008) Ricarda J. C. Hilf et al.   NATURE

Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model

(2008) H. Gong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energetics of Divalent Selectivity in a Calcium Channel: The Ryanodine Receptor Case Study

(2007) Dirk Gillespie   BIOPHYSICAL JOURNAL

Properties of Bacillus cereus hemolysin II: A heptameric transmembrane pore

(2002) George Miles et al.   PROTEIN SCIENCE