(Q42154900)

English

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides (English)

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

author name string

Mikyung Seo

1

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

Sarah Rauscher

2

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

Régis Pomès

3

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

D Peter Tieleman

4

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

publication date

26 March 2012

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

Journal of Chemical Theory and Computation

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

8

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

5

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

1774-1785

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Using the Wimley-White Hydrophobicity Scale as a Direct Quantitative Test of Force Fields: The MARTINI Coarse-Grained Model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Martini Coarse-Grained Force Field: Extension to Carbohydrates.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Structural disorder and dynamics of elastin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Effect of beta-sheet propensity on peptide aggregation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Membrane proteins: molecular dynamics simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Coarse-grained simulation: a high-throughput computational approach to membrane proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

A coarse-grained protein force field for folding and structure prediction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

The MARTINI force field: coarse grained model for biomolecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Multiscale modeling of biomolecular systems: in serial and in parallel

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Recent atomic models of amyloid fibril structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Insertion and assembly of membrane proteins via simulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

GROMACS: fast, flexible, and free

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Structure of the cross-beta spine of amyloid-like fibrils

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Coarse-grained models for proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Computer simulations of membrane proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Synthetic mammalian prions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Temperature-dependent conformational transitions and hydrogen-bond dynamics of the elastin-like octapeptide GVG(VPGVG): a molecular-dynamics study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Protein folding and misfolding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Computer simulation studies of model biological membranes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

NMR solution structure of the human prion protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Canonical dynamics: Equilibrium phase-space distributions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

The cell biology of beta-amyloid precursor protein and presenilin in Alzheimer's disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

29 May 2018

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Distributed Replica Sampling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Computer simulation study of fullerene translocation through lipid membranes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

A coarse grain model for DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Proline and glycine control protein self-organization into elastomeric or amyloid fibrils.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Solution NMR studies of the A beta(1-40) and A beta(1-42) peptides establish that the Met35 oxidation state affects the mechanism of amyloid formation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

17 August 2018

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3348680

3 November 2018

Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

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Molecular mechanism of β-sheet self-organization at water-hydrophobic interfaces

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

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based on heuristic

inferred from PubMed ID database lookup

Biochemistry of tropoelastin

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A coarse-grained protein-protein potential derived from an all-atom force field

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of endogenous amylin in glucagon secretion and gastric emptying in rats demonstrated with the selective antagonist, AC187

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence and Structure Determinants for the Self-aggregation of Recombinant Polypeptides Modeled after Human Elastin

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model

1 reference

https://pubmed.ncbi.nlm.nih.gov/22582033

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/CT200876V

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

release_glayybff6bbi7jj655yxmtt5au

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https://api.fatcat.wiki/v0/release/glayybff6bbi7jj655yxmtt5au

24 November 2022

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mapped directly with Wikidata item

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

17 October 2017

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