(Q34982184)

5 August 2017

title

Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding (English)

1 reference

5 August 2017

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6

1 reference

5 August 2017

Gennady M Verkhivker

1

1 reference

5 August 2017

Djamal Bouzida

2

1 reference

5 August 2017

Daniel K Gehlhaar

3

1 reference

5 August 2017

Paul A Rejto

4

1 reference

5 August 2017

Stephan T Freer

5

1 reference

5 August 2017

language of work or name

English

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publication date

15 April 2003

1 reference

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

5 August 2017

published in

1 reference

5 August 2017

volume

100

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5 August 2017

issue

9

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5 August 2017

page(s)

5148-5153

1 reference

Is there a unifying mechanism for protein folding?

5 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Absolute comparison of simulated and experimental protein-folding dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Natively unfolded proteins: a point where biology waits for physics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Protein folding and unfolding at atomic resolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Coupling of folding and binding for unstructured proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Intrinsically disordered protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Protein folding theory: from lattice to all-atom models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Deciphering common failures in molecular docking of ligand-protein complexes.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

A surprising simplicity to protein folding.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

The energy landscape theory of protein folding: insights into folding mechanisms and scenarios

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

A simple model for calculating the kinetics of protein folding from three-dimensional structures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

A theoretical search for folding/unfolding nuclei in three-dimensional protein structures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Folding and binding cascades: shifts in energy landscapes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Substrate recruitment to cyclin-dependent kinase 2 by a multipurpose docking site on cyclin A.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

"New view" of protein folding reconciled with the old through multiple unfolding simulations.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Coupling of local folding to site-specific binding of proteins to DNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=154313

Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1).

8 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0531373100

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0531373100

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0531373100

On the transition coordinate for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0531373100

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12697905

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Efficient Monte Carlo methods for the computer simulation of biological molecules

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12697905

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0531373100

1 reference

5 August 2017

0 references

1 reference

5 August 2017

1 reference