(Q30164251)

19 September 2017

Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations (English)

1 reference

molecular dynamics simulation

19 September 2017

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0 references

author name string

G Settanni

series ordinal

1

1 reference

19 September 2017

J Gsponer

series ordinal

2

1 reference

19 September 2017

A Caflisch

series ordinal

3

1 reference

19 September 2017

language of work or name

English

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publication date

1 March 2004

1 reference

19 September 2017

1 reference

19 September 2017

86

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19 September 2017

3

1 reference

19 September 2017

1691-1701

1 reference

Fast protein folding on downhill energy landscape

19 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Posttransition state desolvation of the hydrophobic core of the src-SH3 protein 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=1304005

Analysis of the distributed computing approach applied to the folding of a small beta peptide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

The complete folding pathway of a protein from nanoseconds to microseconds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Is there a unifying mechanism for 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=1304005

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=1304005

Surfing on protein folding energy landscapes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Probing the folding free energy landscape of the Src-SH3 protein 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=1304005

Absolute comparison of simulated and experimental protein-folding dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Determination of a transition state at atomic resolution from protein engineering data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

On the simulation of protein folding by short time scale molecular dynamics and distributed computing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding 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=1304005

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

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=1304005

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Hydrophobic core packing in the SH3 domain folding 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=1304005

Evaluation of a fast implicit solvent model for 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=1304005

Role of native topology investigated by multiple unfolding simulations of four SH3 domains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Three key residues form a critical contact network in a protein folding 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=1304005

Folding simulations of a three-stranded antiparallel beta -sheet peptide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Fast kinetics and mechanisms in 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=1304005

Long-range order in the src SH3 folding 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=1304005

Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

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=1304005

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Effective energy function for proteins in solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

De novo design of a monomeric three-stranded antiparallel beta-sheet

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src 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=1304005

Three-dimensional structure of the tyrosine kinase c-Src

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Knowledge-based protein secondary structure assignment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 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=1304005

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Mapping the transition state and pathway of protein folding by protein engineering

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Parallel protein-unfolding pathways revealed and mapped

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Transition states and the meaning of Phi-values in protein folding kinetics

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Critical role of beta-hairpin formation in protein G 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=1304005

A breakdown of symmetry in the folding transition state of protein L

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Structure of the transition state for folding of a protein derived from experiment and simulation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304005

Molecular dynamics with coupling to an external bath

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974238-1

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974238-1

Weak temperature dependence of the free energy surface and folding pathways of structured peptides

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974238-1

Is protein unfolding the reverse of protein folding? A lattice simulation analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974238-1

On the transition coordinate for protein folding

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974238-1

Native topology or specific interactions: what is more important for protein folding?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974238-1

Mathematical analysis of coupled parallel simulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974238-1

10.1016/S0006-3495(04)74238-1

7 January 2021

Identifiers

DOI

1 reference

19 September 2017

1 reference

19 September 2017

PubMed publication ID

14990497

1 reference