(Q31065927)

3 September 2017

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent (English)

1 reference

3 September 2017

1

J Juraszek

1 reference

3 September 2017

P G Bolhuis

2

1 reference

PMC publication ID

1595309

3 September 2017

language of work or name

English

0 references

publication date

11 October 2006

1 reference

Proceedings of the National Academy of Sciences of the United States of America

3 September 2017

1 reference

3 September 2017

103

1 reference

3 September 2017

43

1 reference

3 September 2017

15859-15864

1 reference

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

3 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Phylogeny of protein-folding trajectories reveals a unique pathway to native structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Kinetic pathways of beta-hairpin (un)folding in explicit solvent

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Simulations of the role of water in the protein-folding mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Unifying features in protein-folding mechanisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Trp-cage: Folding free energy landscape in explicit water

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Transition-path sampling of β-hairpin folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Escaping free-energy minima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Drying-induced hydrophobic polymer collapse

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Designing a 20-residue protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Understanding protein folding via free-energy surfaces from theory and experiment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Canonical dynamics: Equilibrium phase-space distributions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

VMD: visual molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1595309

Specific nucleus as the transition state for protein folding: evidence from the lattice model.

21 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

UV-resonance raman thermal unfolding study of Trp-cage shows that it is not a simple two-state miniprotein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

Methods for molecular dynamics simulations of protein folding/unfolding in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

Predicting slow structural transitions in macromolecular systems: Conformational flooding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

Optimal allocation of replicas in parallel tempering simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

On the transition coordinate for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

Automatic method for identifying reaction coordinates in complex systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

The GROMOS Biomolecular Simulation Program Package

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

21 January 2018

Protein-folding dynamics

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0606692103

The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17035504

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Acid and thermal denaturation of barnase investigated by molecular dynamics simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17035504

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0606692103

1 reference

3 September 2017

0 references

1 reference

PMC publication ID

1595309

3 September 2017

PubMed publication ID

17035504

1 reference

PMC publication ID

1595309