Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms. (Q51838935)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19195554%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

title

Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms (English)

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20 January 2020

2

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20 January 2020

Phillip J. Stansfeld

4

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20 January 2020

Mark S.P. Sansom

5

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20 January 2020

Kaihsu Tai

1

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author name string

Kaihsu Tai

1

1 reference

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20 January 2020

Younes Mokrab

3

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20 January 2020

publication date

1 January 2008

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20 January 2020

published in

Methods in Cell Biology

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20 January 2020

volume

90

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20 January 2020

page(s)

233-265

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Energetics of ion conduction through the gramicidin channel

20 January 2020

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A microscopic view of ion conduction through the K+ channel.

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7 January 2021

A gate in the selectivity filter of potassium channels

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Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors

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Permeation through an open channel: Poisson-Nernst-Planck theory of a synthetic ionic channel

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7 January 2021

Prediction of CASP6 structures using automated Robetta protocols

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7 January 2021

The relation between the divergence of sequence and structure in proteins

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7 January 2021

Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel

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7 January 2021

Voltage-dependent gating at the KcsA selectivity filter

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7 January 2021

Molecular driving forces determining potassium channel slow inactivation

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7 January 2021

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

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7 January 2021

Modeling Membranes under a Transmembrane Potential

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7 January 2021

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

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7 January 2021

Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1.

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7 January 2021

The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

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7 January 2021

Rotamer libraries in the 21st century

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7 January 2021

Profile hidden Markov models

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7 January 2021

3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor

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7 January 2021

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

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7 January 2021

Rapid, Accurate, and Precise Calculation of Relative Binding Affinities for the SH2 Domain Using a Computational Grid

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The selectivity of K+ ion channels: testing the hypotheses

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7 January 2021

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7 January 2021

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A hierarchical approach to all-atom protein loop prediction

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7 January 2021

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7 January 2021

Crystal structure and mechanism of a calcium-gated potassium channel

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7 January 2021

The open pore conformation of potassium channels

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7 January 2021

X-ray structure of a voltage-dependent K+ channel

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7 January 2021

A model recognition approach to the prediction of all-helical membrane protein structure and topology

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7 January 2021

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

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7 January 2021

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

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7 January 2021

Progress over the first decade of CASP experiments.

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7 January 2021

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

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7 January 2021

Crystal structure of the potassium channel KirBac1.1 in the closed state

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7 January 2021

Physics of ion channels.

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7 January 2021

Effective energy functions for protein structure prediction.

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7 January 2021

KcsA: it's a potassium channel

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7 January 2021

Accurate modeling of protein conformation by automatic segment matching

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7 January 2021

Is arginine charged in a membrane?

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7 January 2021

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

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7 January 2021

Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment

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7 January 2021

Mechanisms of tetraethylammonium ion block in the KcsA potassium channel

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7 January 2021

Distribution of amino acids in a lipid bilayer from computer simulations.

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The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents

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7 January 2021

Alignment of protein sequences by their profiles

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7 January 2021

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7 January 2021

Structure and gating mechanism of the acetylcholine receptor pore

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7 January 2021

Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor.

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7 January 2021

Stereochemical quality of protein structure coordinates

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7 January 2021

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

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7 January 2021

Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics.

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7 January 2021

SCOP: a structural classification of proteins database for the investigation of sequences and structures

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7 January 2021

Crystal structure of a Kir3.1-prokaryotic Kir channel chimera

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7 January 2021

Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands.

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7 January 2021

Ion selectivity in potassium channels

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7 January 2021

Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels

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7 January 2021

CATH--a hierarchic classification of protein domain structures

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7 January 2021

Polymorphic transitions in single crystals: A new molecular dynamics method

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7 January 2021

Protein structure prediction: inroads to biology.

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7 January 2021

Voltage-sensor activation with a tarantula toxin as cargo.

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7 January 2021

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

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7 January 2021

Side-chain ionization states in a potassium channel

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Enhancing the accuracy, the efficiency and the scope of free energy simulations

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7 January 2021

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

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7 January 2021

Comparative protein modelling by satisfaction of spatial restraints

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7 January 2021

Atomistic simulations of biologically realistic transmembrane potential gradients.

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7 January 2021

SWISS-MODEL: An automated protein homology-modeling server

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7 January 2021

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

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7 January 2021

The GROMOS Biomolecular Simulation Program Package

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7 January 2021

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7 January 2021

Atomic structure of a Na+- and K+-conducting channel

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7 January 2021

Assessing strategies for improved superfamily recognition

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7 January 2021

Recognition of errors in three-dimensional structures of proteins

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7 January 2021

A novel method for structure-based prediction of ion channel conductance properties.

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7 January 2021

Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures

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7 January 2021

On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles

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7 January 2021

In silico research in drug discovery

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7 January 2021

The predominant role of coordination number in potassium channel selectivity

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7 January 2021

K+ conduction in the selectivity filter of potassium channels is monitored by the charge distribution along their sequence

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7 January 2021

Molecular restraints in the permeation pathway of ion channels

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7 January 2021

Refined structure of the nicotinic acetylcholine receptor at 4A resolution

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7 January 2021

GROMACS: fast, flexible, and free

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7 January 2021

Tuning ion coordination architectures to enable selective partitioning

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7 January 2021

K+/Na+ selectivity in K channels and valinomycin: over-coordination versus cavity-size constraints

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7 January 2021

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

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7 January 2021

SGTx1, a Kv channel gating-modifier toxin, binds to the interfacial region of lipid bilayers

1 reference

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7 January 2021

Lipid bilayer deformation and the free energy of interaction of a Kv channel gating-modifier toxin.

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7 January 2021

AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

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7 January 2021

Extending the accuracy limits of prediction for side-chain conformations

1 reference

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7 January 2021

Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution

1 reference

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7 January 2021

10.1016/S0091-679X(08)00812-1

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19195554%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

1 reference