Force field influences in beta-hairpin folding simulations (Q36458088)

14 August 2017

Force field influences in beta-hairpin folding simulations (English)

1 reference

14 August 2017

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Ray Luo

2

0 references

author name string

Thu Zar Lwin

series ordinal

1

1 reference

14 August 2017

1 November 2006

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14 August 2017

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14 August 2017

15

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14 August 2017

11

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14 August 2017

2642-2655

1 reference

Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Transition-path sampling of β-hairpin folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

The free energy landscape for beta hairpin folding in explicit water

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Mechanisms and kinetics of beta-hairpin formation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

A simple model for calculating the kinetics of protein folding from three-dimensional structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Understanding beta-hairpin formation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Folding dynamics and mechanism of beta-hairpin formation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

A molecular dynamics simulation of double-helical B-DNA including counterions and water

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Computational studies of the interaction of myoglobin and xenon

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Molecular dynamics studies of a DNA‐binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Is Poisson-Boltzmann theory insufficient for protein folding simulations?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Complex folding pathways in a simple beta-hairpin

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2242415

Exploring the energy landscape of a beta hairpin in explicit solvent

21 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17075138

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17075138

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

An all atom force field for simulations of proteins and nucleic acids

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17075138

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1110/PS.062438006

1 reference

14 August 2017

1 reference

14 August 2017

1 reference

PMCID

2242415