Determination of membrane-insertion free energies by molecular dynamics simulations (Q35769994)

10 August 2017

Determination of membrane-insertion free energies by molecular dynamics simulations (English)

1 reference

10 August 2017

1

James Gumbart

1 reference

10 August 2017

Benoît Roux

2

1 reference

PubMed ID

22385850

10 August 2017

language of work or name

English

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publication date

21 February 2012

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10 August 2017

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10 August 2017

102

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10 August 2017

4

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10 August 2017

795-801

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PubMed ID

22385850

describes a project that uses

10 August 2017

molecular dynamics simulation

1 reference

based on heuristic

inferred from title

cites work

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1 reference

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

12 July 2018

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Hydrophobicity scales: a thermodynamic looking glass into lipid-protein interactions

12 July 2018

1 reference

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In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions

12 July 2018

1 reference

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Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers

12 July 2018

1 reference

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High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD

12 July 2018

1 reference

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Cryo-EM structure of the ribosome–SecYE complex in the membrane environment

12 July 2018

1 reference

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Free-energy cost for translocon-assisted insertion of membrane proteins

12 July 2018

1 reference

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Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments

12 July 2018

1 reference

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A look at arginine in membranes

12 July 2018

1 reference

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On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes

12 July 2018

1 reference

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Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

12 July 2018

1 reference

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Protein contents in biological membranes can explain abnormal solvation of charged and polar residues

12 July 2018

1 reference

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CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes

12 July 2018

1 reference

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Force field bias in protein folding simulations

12 July 2018

1 reference

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Many-body polarization effects and the membrane dipole potential

12 July 2018

1 reference

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

12 July 2018

1 reference

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A continuum method for determining membrane protein insertion energies and the problem of charged residues

12 July 2018

1 reference

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Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations.

12 July 2018

1 reference

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Automated builder and database of protein/membrane complexes for molecular dynamics simulations

12 July 2018

1 reference

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Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment

12 July 2018

1 reference

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Membrane protein insertion: the biology-physics nexus

12 July 2018

1 reference

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On the thermodynamic stability of a charged arginine side chain in a transmembrane helix

12 July 2018

1 reference

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

12 July 2018

1 reference

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Molecular dynamics studies of the archaeal translocon

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Very fast empirical prediction and rationalization of protein pKa values

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Scalable molecular dynamics with NAMD

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Recognition of transmembrane helices by the endoplasmic reticulum translocon.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Energetics of ion conduction through the gramicidin channel

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Cooperation of transmembrane segments during the integration of a double-spanning protein into the ER membrane

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Structural evidence for dimerization-regulated activation of an integral membrane phospholipase

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

VMD: visual molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

A simple method for displaying the hydropathic character of a protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Good practices in free-energy calculations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

The role of lipid composition for insertion and stabilization of amino acids in membranes.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Molecular code for transmembrane-helix recognition by the Sec61 translocon

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Lonely arginine seeks friendly environment

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Membrane Insertion of Marginally Hydrophobic Transmembrane Helices Depends on Sequence Context

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3283816

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

15 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22385850

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22385850

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2012.01.021

1 reference

10 August 2017

1 reference

10 August 2017

1 reference

PubMed ID

22385850