Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations (Q36039378)

11 August 2017

Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations (English)

1 reference

11 August 2017

5

Klaus Schulten

1 reference

11 August 2017

4

Martin Gruebele

1 reference

11 August 2017

2

Johan Strümpfer

1 reference

11 August 2017

Yanxin Liu

1

1 reference

PMC publication ID

3377354

11 August 2017

Peter L Freddolino

series ordinal

3

1 reference

11 August 2017

11 April 2012

1 reference

Journal of Physical Chemistry Letters

11 August 2017

1 reference

11 August 2017

3

1 reference

11 August 2017

9

1 reference

11 August 2017

1117-1123

1 reference

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

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

The fast and the slow: folding and trapping of λ6-85.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

How fast-folding proteins fold

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Challenges in protein folding simulations: Timescale, representation, and 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=3377354

Computational design and experimental testing of the fastest-folding β-sheet 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=3377354

Atomic-Level Characterization of the Structural Dynamics 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=3377354

Enhanced sampling and applications in protein folding in explicit 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=3377354

Going beyond clustering in MD trajectory analysis: an application to villin headpiece 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=3377354

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Theoretical perspectives on 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=3377354

A Survey of λ Repressor Fragments from Two-State to Downhill 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=3377354

Error and efficiency of replica exchange molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Common structural transitions in explicit-solvent simulations of villin headpiece 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=3377354

Analysis of the free-energy surface of proteins from reversible folding simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Single homopolypeptide chains collapse into mechanically rigid conformations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Force field bias in protein folding simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Coarse-grained models of protein folding: toy models or predictive tools?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Solvent-tuning the collapse and helix formation time scales of lambda(6-85)*.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Scalable molecular dynamics with NAMD

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Kinetics are probe-dependent during downhill folding of an engineered lambda6-85 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=3377354

Empirical force fields for biological macromolecules: overview and issues.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics 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=3377354

The protein folding 'speed limit'.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

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=3377354

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Theory of protein folding: the energy landscape perspective

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Submillisecond folding of monomeric lambda repressor

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Reducing lambda repressor to the core

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

What ice can teach us about water interactions: a critical comparison of the performance of different water models.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Tuning lambda6-85 towards downhill folding at its melting temperature

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3377354

Minimum energy compact structures of random sequences of heteropolymers

5 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22737279

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Folding at the speed limit

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22737279

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JZ300017C

1 reference

11 August 2017

1 reference

PMC publication ID

3377354

11 August 2017

PubMed publication ID

22737279

1 reference

PMC publication ID

3377354