(Q30153502)

19 August 2017

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations (English)

1 reference

molecular dynamics simulation

19 August 2017

0 references

1 reference

3

James C Gumbart

1 reference

19 August 2017

Fatemeh Khalili-Araghi

series ordinal

1

1 reference

19 August 2017

Brigitte Ziervogel

series ordinal

2

1 reference

19 August 2017

Benoît Roux

series ordinal

4

1 reference

19 August 2017

language of work or name

1 reference

1 October 2013

1 reference

The Journal of General Physiology

19 August 2017

1 reference

19 August 2017

142

1 reference

19 August 2017

4

1 reference

19 August 2017

465-475

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Atomic-level simulation of current-voltage relationships in single-file ion channels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Constant electric field simulations of the membrane potential illustrated with simple systems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Brownian dynamics simulations of ion transport through the VDAC.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Principles of conduction and hydrophobic gating in K+ channels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter. II. Multi-ion effects studied with grand canonical Monte Carlo/Brownian dynamics simulations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Understanding ion conductance on a molecular level: an all-atom modeling of the bacterial porin OmpF.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Molecular model of a cell plasma membrane with an asymmetric multicomponent composition: water permeation and ion effects.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Initial response of the potassium channel voltage sensor to a transmembrane potential

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

The membrane potential and its representation by a constant electric field in computer simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Ion conduction through MscS as determined by electrophysiology and simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Dynamics of K+ ion conduction through Kv1.2.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Scalable molecular dynamics with NAMD

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Crystal structure of a mammalian voltage-dependent Shaker family K+ channel

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Theory and simulation of water permeation in aquaporin-1.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Effect of sodium chloride on a lipid bilayer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

VMD: visual molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

The structure of OmpF porin in a tetragonal crystal form

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Ion selectivity of gram-negative bacterial porins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Crystal structures explain functional properties of two E. coli porins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787774

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

3 June 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Information Theory and Statistical Mechanics

21 January 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Rapid screening of membrane protein activity: electrophysiological analysis of OmpF reconstituted in proteoliposomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Atomistic simulations of biologically realistic transmembrane potential gradients.

21 January 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Kinetic pathways of beta-hairpin (un)folding in explicit solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1085%2FJGP.201311014

Molecular dynamics simulation of continuous current flow through a model biological membrane channel

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24081985

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24081985

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Modeling Membranes under a Transmembrane Potential

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24081985

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1085/JGP.201311014

1 reference

19 August 2017

1 reference

19 August 2017

1 reference