(Q41047006)

26 September 2017

Conformational sampling with implicit solvent models: application to the PHF6 peptide in tau protein (English)

1 reference

26 September 2017

Austin Huang

1

1 reference

26 September 2017

Collin M Stultz

series ordinal

2

1 reference

26 September 2017

language of work or name

English

0 references

publication date

13 October 2006

1 reference

26 September 2017

1 reference

26 September 2017

92

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26 September 2017

1

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26 September 2017

34-45

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26 September 2017

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Tau pathology in Alzheimer disease and other tauopathies

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Potential structure/function relationships of predicted secondary structural elements of tau.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Computational protein design is a challenge for implicit solvation models

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Template-assisted filament growth by parallel stacking of tau.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Recent advances in the development and application of implicit solvent models in biomolecule simulations

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Principles of protein folding, misfolding and aggregation

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Tau filaments from human brain and from in vitro assembly of recombinant protein show cross-beta structure

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Conformations of amino acids in proteins.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif ((306)VQIVYK(311)) forming beta structure

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

REVIEW: tau protein pathology in Alzheimer's disease and related disorders

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Discrimination of the native from misfolded protein models with an energy function including implicit solvation

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Effective energy function for proteins in solution

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

VMD: visual molecular dynamics

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

"New view" of protein folding reconciled with the old through multiple unfolding simulations.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Toward absolute density of states calculations for proteins.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Generalized born model with a simple smoothing function.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Identifying native-like protein structures using physics-based potentials

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

MCSS functionality maps for a flexible protein.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Folded conformation of an immunostimulating tetrapeptide rigin: high temperature molecular dynamics simulation study

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1697846

Conformational sampling using high-temperature molecular dynamics

4 November 2018

1 reference

12 December 2020

Localized unfolding of collagen explains collagenase cleavage near imino-poor sites

1 reference

12 December 2020

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme

1 reference

12 December 2020

Potentials of mean force between ionizable amino acid side chains in water

1 reference

12 December 2020

Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: a molecular dynamics study

1 reference

12 December 2020

Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogues

1 reference

12 December 2020

Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta-structure

1 reference

12 December 2020

On the unfolding of alpha-lytic protease and the role of the pro region

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.091207

Identifiers

DOI

1 reference

26 September 2017

1 reference

26 September 2017

PubMed publication ID

17040986

1 reference