(Q34192586)

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Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models

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scholarly article

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Europe PubMed Central

PubMed publication ID

31 July 2017

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models (English)

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Europe PubMed Central

PubMed publication ID

31 July 2017

molecular chaperones

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Alan E Mark

3

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author name string

Hao Fan

1

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Europe PubMed Central

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31 July 2017

Xavier Periole

2

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31 July 2017

language of work or name

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publication date

13 April 2012

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31 July 2017

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31 July 2017

80

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31 July 2017

7

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31 July 2017

1744-1754

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Europe PubMed Central

PubMed publication ID

31 July 2017

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Protein structure prediction and structural genomics

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Comparative protein structure modeling of genes and genomes

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

A surprising simplicity to protein folding.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Ab initio protein structure prediction: progress and prospects.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Toward high-resolution de novo structure prediction for small proteins.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Critical assessment of methods of protein structure prediction - Round VIII.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

I-TASSER: fully automated protein structure prediction in CASP8

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Structure prediction for CASP8 with all-atom refinement using Rosetta.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Assessment of CASP8 structure predictions for template free targets

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

MUFOLD: A new solution for protein 3D structure prediction

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Automated structure prediction of weakly homologous proteins on a genomic scale

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Refinement of homology-based protein structures by molecular dynamics simulation techniques

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Replica Monte Carlo simulation of spin glasses.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Replica-exchange molecular dynamics method for protein folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Generalized-ensemble algorithms for molecular simulations of biopolymers

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Can molecular dynamics simulations provide high-resolution refinement of protein structure?

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Molecular chaperones in cellular protein folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Protein folding in vivo: the importance of molecular chaperones

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Molecular chaperones--cellular machines for protein folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Simulations of chaperone-assisted folding.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Simulations of beta-hairpin folding confined to spherical pores using distributed computing

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: creation of an alternate fast folding pathway

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

SCOP: a structural classification of proteins database for the investigation of sequences and structures

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

GROMACS: A message-passing parallel molecular dynamics implementation

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Efficient sampling of protein structures by model hopping.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Protein structure prediction using Rosetta

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

NMR structure and mutagenesis of the FADD (Mort1) death-effector domain

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Structures of the reduced and mercury-bound forms of MerP, the periplasmic protein from the bacterial mercury detoxification system

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

How fast-folding proteins fold

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

TASSER: an automated method for the prediction of protein tertiary structures in CASP6.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

The protein folding problem: when will it be solved?

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Essential energy space random walks to accelerate molecular dynamics simulations: convergence improvements via an adaptive-length self-healing strategy

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

GROMACS 3.0: a package for molecular simulation and trajectory analysis

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Molecular dynamics with coupling to an external bath

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24068

21 January 2018

Identifiers

10.1002/PROT.24068

1 reference

Europe PubMed Central

PubMed publication ID

31 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

31 July 2017

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