(Q30377510)

12 October 2017

1 reference

title

Folding by numbers: primary sequence statistics and their use in studying protein folding (English)

1 reference

12 October 2017

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0 references

Brent Wathen

1

1 reference

12 October 2017

Zongchao Jia

series ordinal

2

1 reference

12 October 2017

language of work or name

English

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publication date

8 April 2009

1 reference

International Journal of Molecular Sciences

12 October 2017

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12 October 2017

10

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12 October 2017

4

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12 October 2017

1567-1589

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Creative Commons Attribution 4.0 International

12 October 2017

start time

8 April 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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20 June 2018

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20 June 2018

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Improved general regression network for protein domain boundary prediction.

20 June 2018

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Progress from CASP6 to CASP7.

20 June 2018

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Identification of putative domain linkers by a neural network - application to a large sequence database

20 June 2018

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20 June 2018

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Amino acid pairing preferences in parallel beta-sheets in proteins.

20 June 2018

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Progress in modeling of protein structures and interactions

20 June 2018

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Assessment of CASP6 predictions for new and nearly new fold targets

20 June 2018

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Downhill protein folding: evolution meets physics

20 June 2018

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Protein folding: the stepwise assembly of foldon units

20 June 2018

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Natively unfolded proteins

20 June 2018

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Energy landscapes and solved protein-folding problems.

20 June 2018

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beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution.

20 June 2018

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Improved prediction for N-termini of alpha-helices using empirical information

20 June 2018

1 reference

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Sequence-based prediction of protein domains.

20 June 2018

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Designing proteins from the inside out.

20 June 2018

1 reference

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Theory of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Some factors in the interpretation of protein denaturation

20 June 2018

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20 June 2018

https://api.crossref.org/works/10.3390%2FIJMS10041567

The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Pretty good guessing: protein structure prediction at CASP5

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

DomCut: prediction of inter-domain linker regions in amino acid sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Recent advances in helix-coil theory.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

The protein folding problem: a biophysical enigma.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Protein folding in the post-genomic era.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Hydrophobic interactions at the Ccap position of the C-capping motif of alpha-helices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

A test of proposed rules for helix capping: Implications for protein design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Intrinsically disordered protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Sequence complexity of disordered protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Domain size distributions can predict domain boundaries

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Why are "natively unfolded" proteins unstructured under physiologic conditions?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Information content of protein sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Fast kinetics and mechanisms in protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Protein folding intermediates and pathways studied by hydrogen exchange

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Intrahelical side chain interactions in alpha-helices: poor correlation between energetics and frequency

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Folding dynamics and mechanism of beta-hairpin formation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

From Levinthal to pathways to funnels

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

The Shannon information entropy of protein sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Favored and suppressed patterns of hydrophobic and nonhydrophobic amino acids in protein sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Identification, classification, and analysis of beta-bulges in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Structural characteristics and stabilizing principles of bent beta-strands in protein tertiary architectures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Protein folding dynamics: the diffusion-collision model and experimental data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Discovering structural correlations in alpha-helices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

A revised set of potentials for beta-turn formation in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Cooperativity in protein-folding kinetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

N- and C-capping preferences for all 20 amino acids in alpha-helical peptides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Prediction of Protein Structural Classes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Hydrophobic basis of packing in globular proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Nucleation, rapid folding, and globular intrachain regions in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Using known substructures in protein model building and crystallography

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Amino acid preferences for specific locations at the ends of alpha helices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Analysis and prediction of the different types of beta-turn in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Helix signals in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Capping and alpha-helix stability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

A 3D building blocks approach to analyzing and predicting structure of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Unusually stable helix formation in short alanine-based peptides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Statistical distribution of hydrophobic residues along the length of protein chains. Implications for protein folding and evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Beta-breakers: an aperiodic secondary structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Structural patterns in globular proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

The β structure: Inter-strand correlations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Antiparallel and parallel β-strands differ in amino acid residue preferences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding

20 June 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Simplified amino acid alphabets for protein fold recognition and implications for folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

A computational approach to simplifying the protein folding alphabet.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

A Mathematical Theory of Communication

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Exploring the sequence patterns in the alpha-helices of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Analysis of gammabeta, betagamma, gammagamma, betabeta multiple turns in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Periodicity in alpha-helix lengths and C-capping preferences.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Kinetic role of helix caps in protein folding is context-dependent

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Propensities, probabilities, and the Boltzmann hypothesis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Side-chain interactions between sulfur-containing amino acids and phenylalanine in alpha-helices.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Stabilizing nonpolar/polar side-chain interactions in the alpha-helix

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Determinants of strand register in antiparallel beta-sheets of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Contributions of residue pairing to beta-sheet formation: conservation and covariation of amino acid residue pairs on antiparallel beta-strands.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Sequence-based protein domain boundary prediction using BP neural network with various property profiles.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Prediction of protein domain boundaries from sequence alone

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Prediction of protein (domain) structural classes based on amino-acid index.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Prediction of protein structural class by amino acid and polypeptide composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Amino acid pairing at the N- and C-termini of helical segments in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Side-chain structures in the first turn of the α-helix 1 1Edited by J. M. Thornton

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Intrahelical side chain-side chain contacts: the consequences of restricted rotameric states and implications for helix engineering and design

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS10041567

Prediction of the protein structural class by specific peptide frequencies

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

The dependence of amino acid pair correlations on structural environment.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680634

Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins

26 November 2018

1 reference

12 December 2020

Analysis and prediction of protein beta-sheet structures by a combinatorial approach

1 reference

12 December 2020

Specific recognition in the tertiary structure of beta-sheets of proteins

1 reference

12 December 2020

The folding type of a protein is relevant to the amino acid composition

1 reference

12 December 2020

Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces

1 reference

12 December 2020

Helix stop and start signals in peptides and proteins. The capping box does not necessarily prevent helix elongation

1 reference

12 December 2020

Domain boundary prediction based on profile domain linker propensity index

1 reference

12 December 2020

Identifiers

DOI

10.3390/IJMS10041567

1 reference

12 October 2017

1 reference

12 October 2017

PubMed publication ID

19468326

1 reference