P versus Q: structural reaction coordinates capture protein folding on smooth landscapes (Q30159963)

1 October 2017

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes (English)

1 reference

1 October 2017

0 references

3

Peter G Wolynes

1 reference

1 October 2017

Samuel S Cho

1

1 reference

PMCID

1334664

1 October 2017

Yaakov Levy

series ordinal

2

1 reference

PMCID

1334664

1 October 2017

language of work or name

English

0 references

publication date

9 January 2006

1 reference

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

1 October 2017

1 reference

1 October 2017

103

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1 October 2017

3

1 reference

1 October 2017

586-591

1 reference

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Nucleation and the transition state of the SH3 domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

How well can simulation predict protein folding kinetics and thermodynamics?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Reaction coordinates and rates from transition paths

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Phi-value analysis by molecular dynamics simulations of reversible folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Folding of a designed simple ankyrin repeat protein.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Three-body interactions improve the prediction of rate and mechanism in protein folding models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Flipping the switch from monomeric to dimeric CV-N has little effect on antiviral activity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Theory of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Protein topology determines binding mechanism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Direct molecular dynamics observation of protein folding transition state ensemble

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Consensus-derived structural determinants of the ankyrin repeat motif

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Topological determinants of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Molecular dynamics simulations of protein folding from the transition state

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Protein folding theory: from lattice to all-atom models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Experiment and theory highlight role of native state topology in SH3 folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Structural correlations in protein folding funnels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Rate theories and puzzles of hemeprotein kinetics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Protein folding funnels: the nature of the transition state ensemble

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1334664

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16407126

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Estimation of protein folding probability from equilibrium simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16407126

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0509768103

1 reference

1 October 2017

0 references

1 reference

1 October 2017

1 reference

PMCID

1334664