Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations (Q42420038)

30 October 2017

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations (English)

1 reference

30 October 2017

0 references

1 reference

3

Valerie Daggett

1 reference

30 October 2017

David A C Beck

1

1 reference

PMC publication ID

1945213

30 October 2017

George W N White

series ordinal

2

1 reference

30 October 2017

11 October 2006

1 reference

Journal of Structural Biology

30 October 2017

1 reference

30 October 2017

157

1 reference

30 October 2017

3

1 reference

30 October 2017

514-523

1 reference

Simulations of the pressure and temperature unfolding of an alpha-helical peptide.

30 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Protein folding pathways from replica exchange simulations and a kinetic network model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Equilibrium structure and folding of a helix-forming peptide: circular dichroism measurements and replica-exchange molecular dynamics simulations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

UCSF Chimera--a visualization system for exploratory research and analysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Trp-cage: Folding free energy landscape in explicit water

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

The complete folding pathway of a protein from nanoseconds to microseconds

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Molecular dynamics simulations of the protein unfolding/folding reaction

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Designing a 20-residue protein

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

The free energy landscape for beta hairpin folding in explicit water

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

The interpretation of protein structures: Estimation of static accessibility

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Convergence of replica exchange molecular dynamics.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Increasing temperature accelerates protein unfolding without changing the pathway of unfolding

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1945213

Exploring the energy landscape of a beta hairpin in explicit solvent

16 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17113307

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.JSB.2006.10.002

1 reference

30 October 2017

1 reference

PMC publication ID

1945213

30 October 2017

PubMed publication ID

17113307

1 reference

PMC publication ID

1945213