(Q21145688)

6 July 2017

title

Folding very short peptides using molecular dynamics (English)

1 reference

molecular dynamics simulation

6 July 2017

main subject

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2

Ken A Dill

Ken A

Dill

1 reference

6 July 2017

Bosco K Ho

1

Bosco K

Ho

1 reference

6 July 2017

language of work or name

English

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publication date

14 April 2006

1 reference

PLOS Computational Biology

6 July 2017

published in

1 reference

6 July 2017

volume

2

1 reference

6 July 2017

issue

4

1 reference

6 July 2017

page(s)

e27

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Creative Commons Attribution 4.0 International

6 July 2017

copyright license

start time

14 April 2006

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Predictions without templates: New folds, secondary structure, and contacts in CASP5

1 reference

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Free energy landscape of protein folding in water: Explicit vs. implicit solvent

19 March 2017

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Stereochemistry of polypeptide chain configurations

19 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

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

19 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

19 March 2017

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Understanding the key factors that control the rate of beta-hairpin folding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Clustering of protein structural fragments reveals modular building block approach of nature.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Revisiting the Ramachandran plot: Hard‐sphere repulsion, electrostatics, and H‐bonding in the α‐helix

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Helix propensities of short peptides: molecular dynamics versus bioinformatics.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Small libraries of protein fragments model native protein structures accurately.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Mechanisms and kinetics of beta-hairpin formation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Is protein folding hierarchic? I. Local structure and peptide folding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Prediction of local structure in proteins using a library of sequence-structure motifs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Folding dynamics and mechanism of beta-hairpin formation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: secondary structure propensities are not conserved in proteins with the same fold

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Experimentally observed conformation-dependent geometry and hidden strain in proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Local sequence-structure correlations in proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Global properties of the mapping between local amino acid sequence and local structure in proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Cooperativity in protein-folding kinetics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native β-hairpin

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

The hydrophobic moment detects periodicity in protein hydrophobicity

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Unusually stable helix formation in short alanine-based peptides

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Autonomous folding of a peptide corresponding to the N-terminal beta-hairpin from ubiquitin

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Equilibrium NMR studies of unfolded and partially folded proteins

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Unfolding of an ?-helix in water

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Ab initio prediction of helical segments in polypeptides.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Determination of the conformation of folding initiation sites in proteins by computer simulation.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Elucidating the folding problem of helical peptides using empirical parameters

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

LINUS: a hierarchic procedure to predict the fold of a protein.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1435986

Energy landscape of a small peptide revealed by dihedral angle principal component analysis

29 November 2018

1 reference

12 December 2020

Theory and applications of the generalized Born solvation model in macromolecular simulations

1 reference

12 December 2020

Water-inserted alpha-helical segments implicate reverse turns as folding intermediates

1 reference

12 December 2020

Hydrogen bond strength and beta-sheet propensities: the role of a side chain blocking effect

1 reference

12 December 2020

Context-dependent secondary structure formation of a designed protein sequence

1 reference

12 December 2020

Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations

1 reference

12 December 2020

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation

1 reference

12 December 2020

Protein design by binary patterning of polar and nonpolar amino acids

1 reference

12 December 2020

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.0020027

7 January 2021

Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulations

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.0020027

7 January 2021

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.0020027

7 January 2021

Replica-exchange molecular dynamics method for protein folding

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.0020027

7 January 2021

10.1371/JOURNAL.PCBI.0020027

Identifiers

DOI

1 reference

6 July 2017

DBLP publication ID

journals/ploscb/HoD06

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

6 July 2017

1 reference