Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences (Q34492990)

2 August 2017

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences (English)

1 reference

2 August 2017

1 reference

Robert B Best

1

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author name string

Jeetain Mittal

series ordinal

2

1 reference

PubMed ID

21322056

2 August 2017

language of work or name

English

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publication date

14 February 2011

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2 August 2017

1 reference

2 August 2017

79

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2 August 2017

4

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2 August 2017

1318-1328

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

2 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Coordinate-dependent diffusion in protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Fast and accurate predictions of protein NMR chemical shifts from interatomic distances.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Force field bias in protein folding simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Thermodynamics and kinetics of protein folding under confinement

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Are current molecular dynamics force fields too helical?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Effect of flexibility and cis residues in single-molecule FRET studies of polyproline

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Comparison of multiple Amber force fields and development of improved protein backbone parameters

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

A general purpose model for the condensed phases of water: TIP4P/2005

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Hairpin folding rates reflect mutations within and remote from the turn region

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Protein folding pathways from replica exchange simulations and a kinetic network model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Kinetic pathways of beta-hairpin (un)folding in explicit solvent

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Hidden complexity of free energy surfaces for peptide (protein) folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Empirical force fields for biological macromolecules: overview and issues.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

The protein folding 'speed limit'.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Trp-cage: Folding free energy landscape in explicit water

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Transition-path sampling of β-hairpin folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Absolute comparison of simulated and experimental protein-folding dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

The free energy landscape for beta hairpin folding in explicit water

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Structural and dynamic characterization of an unfolded state of poplar apo-plastocyanin formed under nondenaturing conditions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Mechanisms and kinetics of beta-hairpin formation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Understanding beta-hairpin formation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Folding dynamics and mechanism of beta-hairpin formation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4228318

Folding of the GB1 hairpin peptide from discrete path sampling.

6 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Complex folding pathways in a simple beta-hairpin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Theoretical characterization of alpha-helix and beta-hairpin folding kinetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Molecular dynamics as a tool to detect protein foldability. A mutant of domain B1 of protein G with non-native secondary structure propensities

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22972

Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus

21 January 2018

1 reference

12 December 2020

Exploring the energy landscape of a beta hairpin in explicit solvent

1 reference

12 December 2020

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation

1 reference

12 December 2020

Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy

1 reference

12 December 2020

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

1 reference

12 December 2020

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

1 reference

12 December 2020

Balance between α and β Structures in Ab Initio Protein Folding

1 reference

12 December 2020

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

1 reference

12 December 2020

Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.22972

1 reference

2 August 2017

1 reference

2 August 2017

1 reference

PubMed ID

21322056