(Q34480062)

2 August 2017

title

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study (English)

1 reference

protein structure prediction

2 August 2017

main subject

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0 references

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George Chikenji

1

1 reference

2 August 2017

Yoshimi Fujitsuka

series ordinal

2

1 reference

2 August 2017

Shoji Takada

series ordinal

3

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2 August 2017

language of work or name

English

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publication date

17 February 2006

1 reference

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

2 August 2017

published in

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2 August 2017

volume

103

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2 August 2017

issue

9

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2 August 2017

page(s)

3141-3146

1 reference

Statistical coil model of the unfolded state: resolving the reconciliation problem

2 August 2017

cites work

1 reference

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6 July 2018

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6 July 2018

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6 July 2018

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Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

6 July 2018

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Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

6 July 2018

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Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments

6 July 2018

1 reference

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6 July 2018

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Role of local sequence in the folding of cellular retinoic abinding protein I: structural propensities of reverse turns

6 July 2018

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De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification

6 July 2018

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Simulations of beta-hairpin folding confined to spherical pores using distributed computing

6 July 2018

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Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations

6 July 2018

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6 July 2018

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Is the unfolded state the Rosetta Stone of the protein folding problem?

6 July 2018

1 reference

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

6 July 2018

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6 July 2018

1 reference

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

6 July 2018

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Solution structure and dynamics of a de novo designed three-helix bundle protein

6 July 2018

1 reference

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Prediction and structural characterization of an independently folding substructure in the src SH3 domain.

6 July 2018

1 reference

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Clustering of low-energy conformations near the native structures of small proteins

6 July 2018

1 reference

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De novo protein design: fully automated sequence selection

6 July 2018

1 reference

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

6 July 2018

1 reference

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The concept of a random coil. Residual structure in peptides and denatured proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Structural correlations in protein folding funnels

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Searching databases of conserved sequence regions by aligning protein multiple-alignments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Funnels, pathways, and the energy landscape of protein folding: a synthesis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Theoretical Studies of Protein Folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Using known substructures in protein model building and crystallography

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Origins of structure in globular proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Dominant forces in protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Accurate modeling of protein conformation by automatic segment matching

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Optimizing physical energy functions for protein folding.

6 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

An analysis of the helix-to-strand transition between peptides with identical sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

Free energy landscapes of peptides by enhanced conformational sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

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.0508195103

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

Protein design: a perspective from simple tractable models

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

Persistence of native-like topology in a denatured protein in 8 M urea

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

Emergence of Preferred Structures in a Simple Model of Protein Folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1413881

Assembling novel protein folds from super-secondary structural fragments

27 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0508195103

Predicting interresidue contacts using templates and pathways

21 January 2018

1 reference

12 December 2020

Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties

1 reference

12 December 2020

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

1 reference

12 December 2020

1 reference

12 December 2020

Residual helical and turn structure in the denatured state of staphylococcal nuclease: analysis of peptide fragments

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0508195103

1 reference

2 August 2017

0 references

1 reference

2 August 2017

1 reference