(Q36036240)

11 August 2017

Hidden protein folding pathways in free-energy landscapes uncovered by network analysis (English)

1 reference

11 August 2017

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1 reference

4

Harold A Scheraga

1 reference

11 August 2017

3

Adam Liwo

1 reference

11 August 2017

Yanping Yin

1

1 reference

PMC publication ID

3376395

11 August 2017

Gia G Maisuradze

series ordinal

2

1 reference

11 August 2017

24 February 2012

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Journal of Chemical Theory and Computation

11 August 2017

1 reference

11 August 2017

8

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11 August 2017

4

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11 August 2017

1176-1189

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Relation between free energy landscapes of proteins and dynamics

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Protein dynamics investigated by inherent structure analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Complex network analysis of free-energy landscapes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Finding community structure in very large networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Testing protein-folding simulations by experiment: B domain of protein A.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Network biology: understanding the cell's functional organization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Community structure in social and biological networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

An efficient algorithm for large-scale detection of protein families

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

The free energy landscape for beta hairpin folding in explicit water

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

The structure of scientific collaboration networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Global optimization of clusters, crystals, and biomolecules.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Exploring the folding free energy surface of a three-helix bundle protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Absence of a stable intermediate on the folding pathway of protein A.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

‘Molten‐globule state’: a compact form of globular proteins with mobile side‐chains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

The Energy Landscapes and Motions of Proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

How complex is the dynamics of Peptide folding?

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Transition state ensemble for the folding of B domain of protein A: a comparison of distributed molecular dynamics simulations with experiments.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

Preorganized secondary structure as an important determinant of fast protein folding

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3376395

First-principles calculation of the folding free energy of a three-helix bundle protein

23 September 2018

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

12 December 2020

Statistical thermodynamics. Taking a walk on a landscape

1 reference

12 December 2020

How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?

1 reference

12 December 2020

Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model

1 reference

12 December 2020

Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT200806N

1 reference

11 August 2017

1 reference

PMC publication ID

3376395

11 August 2017

PubMed publication ID

22715321

1 reference

PMC publication ID

3376395