Polarizable water model for the coarse-grained MARTINI force field (Q33604854)

28 July 2017

Polarizable water model for the coarse-grained MARTINI force field (English)

1 reference

28 July 2017

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3

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Semen O. Yesylevskyy

series ordinal

1

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Lars V Schäfer

object named as

Lars V Schäfer

series ordinal

2

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Siewert J Marrink

object named as

Siewert J Marrink

series ordinal

4

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publication date

10 June 2010

1 reference

PLOS Computational Biology

28 July 2017

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28 July 2017

6

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28 July 2017

6

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28 July 2017

e1000810

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Creative Commons Attribution 4.0 International

28 July 2017

start time

10 June 2010

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Polarizable Force Fields: History, Test Cases, and Prospects

1 reference

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Martini Coarse-Grained Force Field: Extension to Carbohydrates.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Current status of the AMOEBA polarizable force field

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

The MARTINI force field: coarse grained model for biomolecular simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Mechanisms of passive ion permeation through lipid bilayers: insights from simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels

28 July 2018

1 reference

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A photochemical technique for measuring lateral diffusion of spin-labeled phospholipids in membranes

28 July 2018

1 reference

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GROMACS: fast, flexible, and free

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Membrane electroporation: a molecular dynamics simulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

The molecular basis of electroporation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Effect of sodium chloride on a lipid bilayer

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Simulation of pore formation in lipid bilayers by mechanical stress and electric fields

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

VMD: visual molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Molecular origin of the internal dipole potential in lipid bilayers: calculation of the electrostatic potential

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Computer simulation of protein folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

Lipid lateral diffusion by pulsed nuclear magnetic resonance

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2883601

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

21 January 2018

Polarizable force fields

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

The missing term in effective pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Membrane potential and electrostatics of phospholipid bilayers with asymmetric transmembrane distribution of anionic lipids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Nanosecond field alignment of head group and water dipoles in electroporating phospholipid bilayers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Mechanism of unassisted ion transport across membrane bilayers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Coarse-grained simulations of the membrane-active antimicrobial Peptide maculatin 1.1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

A simple polarizable model of water based on classical Drude oscillators

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000810

Multiscale modeling of lipids and lipid bilayers

21 January 2018

1 reference

12 December 2020

Phase Behavior of Model Lipid Bilayers†

1 reference

12 December 2020

Pore Formation Coupled to Ion Transport through Lipid Membranes as Induced by Transmembrane Ionic Charge Imbalance: Atomistic Molecular Dynamics Study

1 reference

12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry

1 reference

12 December 2020

Osmotic coefficients of atomistic NaCl (aq) force fields

1 reference

12 December 2020

A quantitative coarse-grain model for lipid bilayers

1 reference

12 December 2020

Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1000810

Identifiers

DOI

1 reference

journals/ploscb/YesylevskyySSM10

28 July 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

28 July 2017

1 reference

PubMed ID

20548957