(Q42430181)

English

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

scientific article published on October 2005

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scholarly article

1 reference

Europe PubMed Central

31 October 2017

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels (English)

1 reference

Europe PubMed Central

31 October 2017

2

object named as

Arieh Warshel

1 reference

Europe PubMed Central

31 October 2017

author name string

Mitsunori Kato

1

1 reference

Europe PubMed Central

31 October 2017

language of work or name

0 references

publication date

1 October 2005

1 reference

Europe PubMed Central

31 October 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

31 October 2017

109

1 reference

Europe PubMed Central

31 October 2017

19516-19522

1 reference

Europe PubMed Central

31 October 2017

41

1 reference

Europe PubMed Central

31 October 2017

Ions and blockers in potassium channels: insights from free energy simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

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

1 reference

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28 May 2018

Why does the Ras switch "break" by oncogenic mutations?

1 reference

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28 May 2018

Modeling diverse range of potassium channels with Brownian dynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Mechanical force generation by G proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

KcsA: it's a potassium channel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

K(+)/Na(+) selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Gating of voltage-dependent potassium channels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Side-chain ionization states in a potassium channel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

A computational study of ion binding and protonation states in the KcsA potassium channel.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Ion permeation mechanism of the potassium channel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Permeation of ions across the potassium channel: Brownian dynamics studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Sodium in gramicidin: an example of a permion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Conduction and selectivity in potassium channels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Structure and dynamics of ion transport through gramicidin A.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Calculations of electrostatic interactions in biological systems and in solutions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Ion transport through pores: A rate-theory analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Interpretation of biological ion channel flux data--reaction-rate versus continuum theory

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

28 May 2018

Tryptophan-47 rotational isomerization in variant-3 scorpion neurotoxin. A combination thermodynamic perturbation and umbrella sampling study

1 reference

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28 May 2018

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

1 reference

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28 May 2018

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

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28 May 2018

Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

16 August 2018

Assessing the efficiency of free energy calculation methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

16 August 2018

Exploring the origin of the ion selectivity of the KcsA potassium channel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

16 August 2018

Electrostatic interactions in an integral membrane protein

1 reference

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16 August 2018

Simulations of ion current in realistic models of ion channels: the KcsA potassium channel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

16 August 2018

Energetics of ion conduction through the K+ channel.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2531223

16 August 2018

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

1 reference

https://pubmed.ncbi.nlm.nih.gov/16853521

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

1 reference

https://pubmed.ncbi.nlm.nih.gov/16853521

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP053208L

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP053208L

Nonequilibrium Equality for Free Energy Differences

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP053208L

Identifiers

10.1021/JP053208L

1 reference

Europe PubMed Central

31 October 2017

1 reference

Europe PubMed Central

31 October 2017

1 reference

Europe PubMed Central

31 October 2017

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