(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)

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

2

1 reference

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20 January 2020

Phillip J. Stansfeld

4

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

Mark S.P. Sansom

5

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

Kaihsu Tai

1

0 references

author name string

Kaihsu Tai

1

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

Younes Mokrab

3

1 reference

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20 January 2020

publication date

1 January 2008

1 reference

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20 January 2020

published in

Methods in Cell Biology

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

volume

90

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

page(s)

233-265

1 reference

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

Energetics of ion conduction through the gramicidin channel

20 January 2020

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7 January 2021

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

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7 January 2021

Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields

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7 January 2021

Structure and function in bacteriorhodopsin: the effect of the interhelical loops on the protein folding kinetics

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7 January 2021

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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7 January 2021

The α7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics.

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7 January 2021

Ion permeation mechanism of the potassium channel

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7 January 2021

Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity

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7 January 2021

Electrostatics of nanosystems: application to microtubules and the ribosome

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7 January 2021

Very fast prediction and rationalization of pKa values for protein-ligand complexes

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7 January 2021

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

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7 January 2021

A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor

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7 January 2021

Not Ions Alone: Barriers to Ion Permeation in Nanopores and Channels

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7 January 2021

Molecular dynamics with coupling to an external bath

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7 January 2021

Announcing the worldwide Protein Data Bank

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7 January 2021

The Protein Data Bank

1 reference

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7 January 2021

Energetics of ion conduction through the K+ channel

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7 January 2021

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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7 January 2021

Predicting transmembrane beta-barrels in proteomes

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7 January 2021

Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state

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7 January 2021

Toward high-resolution de novo structure prediction for small proteins.

1 reference

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7 January 2021

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

1 reference

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7 January 2021

Expectations from structural genomics

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7 January 2021

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Prediction of CASP6 structures using automated Robetta protocols

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

The relation between the divergence of sequence and structure in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Voltage-dependent gating at the KcsA selectivity filter

1 reference

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7 January 2021

Molecular driving forces determining potassium channel slow inactivation

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Modeling Membranes under a Transmembrane Potential

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Rotamer libraries in the 21st century

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Profile hidden Markov models

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

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7 January 2021

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

1 reference

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7 January 2021

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

1 reference

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7 January 2021

The selectivity of K+ ion channels: testing the hypotheses

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7 January 2021

Comparative modeling for protein structure prediction

1 reference

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7 January 2021

Principles of selective ion transport in channels and pumps

1 reference

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7 January 2021

Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations.

1 reference

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7 January 2021

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

1 reference

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7 January 2021

Overcoming free energy barriers using unconstrained molecular dynamics simulations

1 reference

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7 January 2021

Classical electrostatics in biology and chemistry

1 reference

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7 January 2021

VMD: visual molecular dynamics

1 reference

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7 January 2021

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

1 reference

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7 January 2021

A hierarchical approach to all-atom protein loop prediction

1 reference

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7 January 2021

Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach

1 reference

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7 January 2021

Crystal structure and mechanism of a calcium-gated potassium channel

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

The open pore conformation of potassium channels

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Progress over the first decade of CASP experiments.

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

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7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Physics of ion channels.

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Effective energy functions for protein structure prediction.

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

KcsA: it's a potassium channel

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Accurate modeling of protein conformation by automatic segment matching

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Is arginine charged in a membrane?

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Mechanisms of tetraethylammonium ion block in the KcsA potassium channel

1 reference

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7 January 2021

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

1 reference

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7 January 2021

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

1 reference

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7 January 2021

Alignment of protein sequences by their profiles

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7 January 2021

Raster3D: photorealistic molecular graphics

1 reference

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7 January 2021

Structure and gating mechanism of the acetylcholine receptor pore

1 reference

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7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Stereochemical quality of protein structure coordinates

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

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7 January 2021

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

1 reference

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7 January 2021

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

1 reference

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7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Ion selectivity in potassium channels

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

CATH--a hierarchic classification of protein domain structures

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Polymorphic transitions in single crystals: A new molecular dynamics method

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Protein structure prediction: inroads to biology.

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Voltage-sensor activation with a tarantula toxin as cargo.

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Side-chain ionization states in a potassium channel

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Comparative protein modelling by satisfaction of spatial restraints

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Atomistic simulations of biologically realistic transmembrane potential gradients.

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

SWISS-MODEL: An automated protein homology-modeling server

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

The GROMOS Biomolecular Simulation Program Package

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Assessing strategies for improved superfamily recognition

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Recognition of errors in three-dimensional structures of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

In silico research in drug discovery

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

The predominant role of coordination number in potassium channel selectivity

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Molecular restraints in the permeation pathway of ion channels

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Refined structure of the nicotinic acetylcholine receptor at 4A resolution

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

GROMACS: fast, flexible, and free

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Tuning ion coordination architectures to enable selective partitioning

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

Extending the accuracy limits of prediction for side-chain conformations

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0091-679X%2808%2900812-1

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