(Q43066617)

13 November 2017

Multiscale investigation of chemical interference in proteins (English)

1 reference

13 November 2017

Dirar Homouz

2

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author name string

Antonios Samiotakis

series ordinal

1

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PubMed ID

20459186

13 November 2017

Margaret S Cheung

series ordinal

3

1 reference

PubMed ID

20459186

13 November 2017

language of work or name

English

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publication date

1 May 2010

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Journal of Chemical Physics

13 November 2017

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13 November 2017

132

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13 November 2017

17

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13 November 2017

175101

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Macromolecular crowding: an important but neglected aspect of the intracellular environment

13 November 2017

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Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding

21 January 2018

1 reference

Molecular basis of the apparent near ideality of urea solutions

21 January 2018

1 reference

Urea's action on hydrophobic interactions

21 January 2018

1 reference

Solvation in protein folding analysis: Combination of theoretical and experimental approaches

21 January 2018

1 reference

Crowded, cell-like environment induces shape changes in aspherical protein

21 January 2018

1 reference

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

21 January 2018

1 reference

Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin

21 January 2018

1 reference

Absolute comparison of simulated and experimental protein-folding dynamics

21 January 2018

1 reference

Theory of protein folding

21 January 2018

1 reference

Recent advances in implicit solvent-based methods for biomolecular simulations

21 January 2018

1 reference

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

21 January 2018

1 reference

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

21 January 2018

1 reference

Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics.

21 January 2018

1 reference

Nonequilibrium, multiple-timescale simulations of ligand-receptor interactions in structured protein systems.

21 January 2018

1 reference

Designing a 20-residue protein

21 January 2018

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A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein

21 January 2018

1 reference

Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations

21 January 2018

1 reference

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

21 January 2018

1 reference

Computing the stability diagram of the Trp-cage miniprotein

21 January 2018

1 reference

Trp-cage: Folding free energy landscape in explicit water

21 January 2018

1 reference

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

21 January 2018

1 reference

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations

21 January 2018

1 reference

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

21 January 2018

1 reference

Mechanisms and kinetics of beta-hairpin formation

21 January 2018

1 reference

Molecular dynamics simulations of the protein unfolding/folding reaction

21 January 2018

1 reference

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields.

21 January 2018

1 reference

Deriving effective mesoscale potentials from atomistic simulations.

21 January 2018

1 reference

Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously.

21 January 2018

1 reference

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

21 January 2018

1 reference

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

21 January 2018

1 reference

New-generation amber united-atom force field

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

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Replica-exchange molecular dynamics method for protein folding

21 January 2018

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Resolution exchange simulation.

21 January 2018

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Resolution Exchange Simulation with Incremental Coarsening.

21 January 2018

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

21 January 2018

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Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

21 January 2018

1 reference

ART 2: self-organization of stable category recognition codes for analog input patterns.

21 January 2018

1 reference

The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus

21 January 2018

1 reference

Effects of crowding and confinement on the structures of the transition state ensemble in proteins.

21 January 2018

1 reference

Fast procedure for reconstruction of full-atom protein models from reduced representations.

21 January 2018

1 reference

A graph-theory algorithm for rapid protein side-chain prediction

21 January 2018

1 reference

From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

21 January 2018

1 reference

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

21 January 2018

1 reference

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

Molecular dynamics simulations at constant pressure and/or temperature

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.3404401

1 reference

13 November 2017

0 references

1 reference

PubMed ID

20459186