(Q51034898)

English

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

scientific article published on 10 October 2014

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scholarly article

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Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations. (English)

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

Martin Zacharias

2

object named as

Martin Zacharias

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

author name string

Katja Ostermeir

1

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Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

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publication date

10 October 2014

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Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

82

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

12

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

3410-3419

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

How fast-folding proteins fold

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Molecular simulation as an aid to experimentalists.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

1 reference

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21 January 2018

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

1 reference

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21 January 2018

Resolution Exchange Simulation with Incremental Coarsening.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

A bias-exchange approach to protein folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Influence of 8-oxoguanosine on the fine structure of DNA studied with biasing-potential replica exchange simulations

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Analysis of domain motions by approximate normal mode calculations.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Conformational change of proteins arising from normal mode calculations

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Molecular dynamics simulations of peptides and proteins with amplified collective motions

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

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21 January 2018

Crystal structure of a cytokine-binding region of gp130.

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21 January 2018

gp130 activation is regulated by D2-D3 interdomain connectivity.

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21 January 2018

Ligand-induced architecture of the leptin receptor signaling complex

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21 January 2018

Solution structure of cyanovirin-N, a potent HIV-inactivating protein

1 reference

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21 January 2018

Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping

1 reference

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21 January 2018

The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures

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21 January 2018

Cyanovirin-N: a sugar-binding antiviral protein with a new twist

1 reference

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21 January 2018

Comparison of simple potential functions for simulating liquid water

1 reference

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21 January 2018

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

1 reference

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21 January 2018

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

1 reference

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21 January 2018

Interleukin-6-type cytokine signalling through the gp130/Jak/STAT pathway

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21 January 2018

The dynamics of signal triggering in a gp130-receptor complex

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24695

21 January 2018

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

1 reference

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21 January 2018

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

1 reference

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21 January 2018

Identifiers

10.1002/PROT.24695

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

release_kgysbcrk7jgejpsgc4gplxukfm

1 reference

https://api.fatcat.wiki/v0/release/kgysbcrk7jgejpsgc4gplxukfm

24 November 2022

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PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

27 March 2018

http://europepmc.org/abstract/MED/25243707

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