(Q33924818)

30 July 2017

Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics (English)

1 reference

30 July 2017

transmembrane transport

0 references

transmembrane protein

0 references

Aleksei Aksimentiev

3

0 references

author name string

David B Wells

series ordinal

1

1 reference

PubMed ID

17902937

30 July 2017

Volha Abramkina

series ordinal

2

1 reference

PubMed ID

17902937

30 July 2017

language of work or name

English

0 references

publication date

1 September 2007

1 reference

Journal of Chemical Physics

30 July 2017

1 reference

30 July 2017

127

1 reference

30 July 2017

125101

1 reference

30 July 2017

12

1 reference

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

30 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Multi-nanopore force spectroscopy for DNA analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Sequencing single molecules of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Simulation of polymer translocation through protein channels

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Molecular dynamics studies of the archaeal translocon

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

The electromechanics of DNA in a synthetic nanopore

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Scalable molecular dynamics with NAMD

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Interactions of peptides with a protein pore

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

5 July 2018

Nanopore cheminformatics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Microscopic Kinetics of DNA Translocation through synthetic nanopores

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Calculating potentials of mean force from steered molecular dynamics simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Microscopic Mechanism of Antibiotics Translocation through a Porin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Translocation of a single-stranded DNA through a conformationally changing nanopore

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Energetics of ion conduction through the gramicidin channel

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Membrane protein simulations: ion channels and bacterial outer membrane proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

A fast in silico simulation of ion flux through the large-pore channel proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Characterization of nucleic acids by nanopore analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Conformational pathways in the gating of Escherichia coli mechanosensitive channel

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Control of the selectivity of the aquaporin water channel family by global orientational tuning

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Ion channels as molecular coulter counters to probe metabolite transport

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Rapid nanopore discrimination between single polynucleotide molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Driven polymer translocation through a narrow pore

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Characterization of individual polynucleotide molecules using a membrane channel

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

VMD: visual molecular dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Alpha-toxin of Staphylococcus aureus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel

5 July 2018

1 reference

Climatic impact of tropical lowland deforestation on nearby montane cloud forests

21 January 2018

1 reference

The mechanism of proton exclusion in aquaporin channels.

21 January 2018

1 reference

Energetics of ion conduction through the K+ channel.

21 January 2018

1 reference

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

Orientation and interactions of dipolar molecules during transport through OmpF porin

21 January 2018

1 reference

Nonequilibrium Equality for Free Energy Differences

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

Single-molecule analysis of DNA-protein complexes using nanopores

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888542

Simultaneous stochastic sensing of divalent metal ions

29 October 2018

1 reference

12 December 2020

Hydrophilicity of cavities in proteins

1 reference

12 December 2020

Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model

1 reference

12 December 2020

Stochastic detection of enantiomers

1 reference

12 December 2020

Simultaneous multianalyte detection with a nanometer-scale pore

1 reference

12 December 2020

Effect of orientation in translocation of polymers through nanopores

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.2770738

1 reference

30 July 2017

1 reference

30 July 2017

1 reference

PubMed ID

17902937