(Q30165454)

13 September 2017

Molecular dynamics simulations of protein folding from the transition state (English)

1 reference

molecular dynamics simulation

13 September 2017

0 references

protein folding

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author name string

Jörg Gsponer

series ordinal

1

1 reference

PMCID

124469

13 September 2017

Amedeo Caflisch

series ordinal

2

1 reference

PMCID

124469

13 September 2017

language of work or name

English

0 references

publication date

30 April 2002

1 reference

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

13 September 2017

6

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

13 September 2017

99

1 reference

13 September 2017

6719-6724

1 reference

13 September 2017

10

1 reference

Evaluation of a fast implicit solvent model for molecular dynamics simulations

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124469

Using flexible loop mimetics to extend -value analysis to secondary structure interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124469

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=124469

Prediction of folding mechanism for circular-permuted 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=124469

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=124469

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=124469

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=124469

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=124469

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=124469

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=124469

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=124469

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=124469

"New view" of protein folding reconciled with the old through multiple unfolding 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=124469

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=124469

MOLMOL: a program for display and analysis of macromolecular structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124469

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=124469

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=124469

Characterizing transition states in protein folding: an essential step in the puzzle

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=124469

Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding 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=124469

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=124469

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=124469

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.092686399

On the transition coordinate for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.092686399

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.092686399

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.092686399

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/11983864

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.092686399

1 reference

13 September 2017

0 references

1 reference

13 September 2017

1 reference

PMCID

124469