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List of works by Toby W Allen

A model of calcium channels

scientific article published on 01 December 2000

A selectivity filter at the intracellular end of the acid-sensing ion channel pore

scientific article

Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane.

scientific article

Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation

scientific article published on 27 June 2019

Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space

scientific article published on April 28, 2012

Brownian dynamics study of an open-state KcsA potassium channel

scientific article published on December 1, 2001

Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)].

scientific article published in June 2008

Comparison of permeation mechanisms in sodium-selective ion channels

scientific article published on 26 May 2018

Computational Models for Predictive Cardiac Ion Channel Pharmacology.

scientific article published on 5 August 2014

Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations.

scientific article

Electrostatics of deformable lipid membranes

scientific article

Estimation of Potentials of Mean Force from Nonequilibrium Pulling Simulations Using Both Minh-Adib Estimator and Weighted Histogram Analysis Method.

scientific article published on 22 January 2016

Gramicidin A channel as a test ground for molecular dynamics force fields

scientific article

Identification of electric-field-dependent steps in the Na(+),K(+)-pump cycle

scientific article

Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel

scientific article

Ion-induced defect permeation of lipid membranes

scientific article published on February 2014

Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel

scientific article

Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore

scientific article

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

scientific article

Membrane protein structure and function

scientific article published on December 22, 2011

Modeling charged protein side chains in lipid membranes.

scientific article published on 16 July 2007

Modeling diverse range of potassium channels with Brownian dynamics.

scientific article

On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation

scientific article published in December 2004

On the role of anionic lipids in charged protein interactions with membranes

scientific article published on November 10, 2010

On the selective ion binding hypothesis for potassium channels

scientific article published on 19 October 2011

On the thermodynamic stability of a charged arginine side chain in a transmembrane helix

scholarly article

Origins of ion selectivity in potassium channels from the perspective of channel block.

scientific article

Permeation of ions across the potassium channel: Brownian dynamics studies

scientific article

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

scientific article published on 06 February 2021

Positronium states in three-dimensional QED

scientific article published on 01 May 1996

Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel

scientific article published on 12 September 2018

Simulating ion channel activation mechanisms using swarms of trajectories

scientific article published on 19 November 2019

String method solution of the gating pathways for a pentameric ligand-gated ion channel.

scientific article published on 9 May 2017

Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data

scientific article

The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers.

scientific article published on 18 January 2012

The determinants of hydrophobic mismatch response for transmembrane helices

scientific article published on 17 September 2012

The different interactions of lysine and arginine side chains with lipid membranes

scientific article published on 27 September 2013

The role of membrane thickness in charged protein-lipid interactions.

scientific article

The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch.

scientific article

The voltage-sensitive dye RH421 detects a Na+,K+-ATPase conformational change at the membrane surface.

scientific article published on 20 January 2017

Towards a Structural View of Drug Binding to hERG K(+) Channels

scientific article

Understanding Sodium Channel Function and Modulation Using Atomistic Simulations of Bacterial Channel Structures.

scientific article