(Q31149897)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

title

Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

author name string

Andrew Kent

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

Abhishek K Jha

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

language of work or name

English

0 references

publication date

19 March 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

number of pages

12

1 reference

Journal of Physical Chemistry B

inferred from page(s)

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

volume

112

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

issue

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

page(s)

6175-6186

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

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

4 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Amyloid beta-protein monomer structure: a computational and experimental study.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Statistical coil model of the unfolded state: resolving the reconciliation problem

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Folding events in the 21-30 region of amyloid beta-protein (Abeta) studied in silico

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Rotational dynamics account for pH-dependent relaxivities of PAMAM dendrimeric, Gd-based potential MRI contrast agents

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Design and characterization of a membrane permeable N-methyl amino acid-containing peptide that inhibits Abeta1-40 fibrillogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Long time dynamic simulations: exploring the folding pathways of an Alzheimer's amyloid Abeta-peptide

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Probing the origins of increased activity of the E22Q "Dutch" mutant Alzheimer's beta-amyloid peptide

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Simulation study of the structure and dynamics of the Alzheimer's amyloid peptide congener in solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

The Alzheimer's peptide a beta adopts a collapsed coil structure in water

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Fresh and nonfibrillar amyloid beta protein(1-40) induces rapid cellular degeneration in aged human fibroblasts: evidence for AbetaP-channel-mediated cellular toxicity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

The nonfibrillar amyloid beta-peptide induces apoptotic neuronal cell death: involvement of its C-terminal fusogenic domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Diffusible, nonfibrillar ligands derived from Abeta1-42 are potent central nervous system neurotoxins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Kinetic theory of fibrillogenesis of amyloid beta-protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

On the nucleation and growth of amyloid beta-protein fibrils: detection of nuclei and quantitation of rate constants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Alzheimer's disease: a central role for amyloid

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

The interpretation of protein structures: Estimation of static accessibility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Energetic coupling between DNA bending and base pair opening

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Atomic solvation parameters applied to molecular dynamics of proteins in solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Probing amyloid fibril formation of the NFGAIL peptide by computer simulations

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Coarse-grained protein molecular dynamics simulations

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide (10-35).

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

A simple method for faster nonbonded force evaluations

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Insights into amyloid structural formation and assembly through computational approaches

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Kinetics of the coil-to-helix transition on a rough energy landscape.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Elucidation of primary structure elements controlling early amyloid beta-protein oligomerization.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Distance and exposure dependent effective dielectric function

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Inhibition of beta-amyloid(40) fibrillogenesis and disassembly of beta-amyloid(40) fibrils by short beta-amyloid congeners containing N-methyl amino acids at alternate residues

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Protofibrillar intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Deposition of monomeric, not oligomeric, Abeta mediates growth of Alzheimer's disease amyloid plaques in human brain preparations.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719849

Amyloid beta-protein fibrillogenesis. Structure and biological activity of protofibrillar intermediates

31 October 2018

1 reference

12 December 2020

Misfolded free energy surface of a peptide with alphabetabeta motif (1PSV) using the generalized Born solvation model

1 reference

12 December 2020

Contact model for the prediction of NMR N-H order parameters in globular proteins

1 reference

12 December 2020

Amyloid beta-peptide oligomerization in silico: dimer and trimer

1 reference

12 December 2020

Replica exchange molecular dynamics simulations of amyloid peptide aggregation

1 reference

12 December 2020

Internal dynamics of human ubiquitin revealed by 13C-relaxation studies of randomly fractionally labeled protein

1 reference

12 December 2020

All-atom fast protein folding simulations: the villin headpiece

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP077099H

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18348560%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

PubMed publication ID

18348560

1 reference