TIGER2: an improved algorithm for temperature intervals with global exchange of replicas (Q37285420)

19 August 2017

TIGER2: an improved algorithm for temperature intervals with global exchange of replicas (English)

1 reference

19 August 2017

Xianfeng Li

1

1 reference

19 August 2017

Robert A Latour

series ordinal

2

1 reference

19 August 2017

Steven J Stuart

series ordinal

3

1 reference

19 August 2017

language of work or name

English

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publication date

1 May 2009

1 reference

Journal of Chemical Physics

19 August 2017

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19 August 2017

130

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19 August 2017

17

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19 August 2017

174106

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

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

A molecular jump mechanism of water reorientation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

10 residue folded peptide designed by segment statistics.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Stereochemistry of polypeptide chain configurations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

The free energy landscape for beta hairpin folding in explicit water

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Unified Approach for Molecular Dynamics and Density-Functional Theory

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Canonical dynamics: Equilibrium phase-space distributions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Dynamic weighting in Monte Carlo and optimization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Curious structure in "canonical" alanine-based peptides

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Folding landscapes of the Alzheimer amyloid-beta(12-28) peptide.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Generalized born model with a simple smoothing function.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2719473

Replica-exchange molecular dynamics method for protein folding

3 September 2018

1 reference

Computer simulation of local order in condensed phases of silicon

21 January 2018

1 reference

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

Molecular dynamics simulations at constant pressure and/or temperature

21 January 2018

1 reference

Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing

21 January 2018

1 reference

Exploring the energy landscape of a beta hairpin in explicit solvent

21 January 2018

1 reference

12 December 2020

An improved replica-exchange sampling method: temperature intervals with global energy reassignment

1 reference

12 December 2020

Molecular dynamics simulations of synthetic peptide folding

1 reference

12 December 2020

Folding free-energy landscape of a 10-residue mini-protein, chignolin

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3129342

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

19425768

1 reference