(Q30367051)

13 October 2017

How a spatial arrangement of secondary structure elements is dispersed in the universe of protein folds. (English)

1 reference

13 October 2017

0 references

1 reference

Shintaro Minami

1

1 reference

13 October 2017

Kengo Sawada

series ordinal

2

1 reference

13 October 2017

George Chikenji

series ordinal

3

1 reference

13 October 2017

language of work or name

English

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publication date

22 September 2014

1 reference

13 October 2017

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13 October 2017

9

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13 October 2017

9

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13 October 2017

e107959

1 reference

Creative Commons Attribution 4.0 International

13 October 2017

start time

22 September 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Using structure to explore the sequence alignment space of remote homologs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

A rewired green fluorescent protein: folding and function in a nonsequential, noncircular GFP permutant

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Studies on the inference of protein binding regions across fold space based on structural similarities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Structural classification of proteins and structural genomics: new insights into protein folding and evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

How significant is a protein structure similarity with TM-score = 0.5?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

The continuity of protein structure space is an intrinsic property of 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=4171485

Probing the "dark matter" of protein fold space.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Discrete-continuous duality of protein structure space.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein 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=4171485

CPDB: a database of circular permutation in 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=4171485

Novel protein folds and their nonsequential structural analogs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Cradle-loop barrels and the concept of metafolds in protein classification by natural descent.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

A comprehensive analysis of non-sequential alignments between all protein 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=4171485

Data growth and its impact on the SCOP database: new developments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Accuracy of structure-based sequence alignment of automatic methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

A comprehensive system for evaluation of remote sequence similarity detection

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Statistics of knots, geometry of conformations, and evolution of 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=4171485

Favin versus concanavalin A: Circularly permuted amino acid sequences

3 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

3 June 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0107959

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Less is more: towards an optimal universal description of protein folds.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Toward high-resolution de novo structure prediction for small 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=4171485

TM-align: a protein structure alignment algorithm based on the TM-score

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

FAST: a novel protein structure alignment algorithm.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Protein homology detection by HMM-HMM comparison

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Non-sequential structure-based alignments reveal topology-independent core packing arrangements in 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=4171485

Scoring function for automated assessment of protein structure template quality

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

MASS: multiple structural alignment by secondary 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=4171485

A global representation of the protein fold space

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Expanding protein universe and its origin from the biological Big Bang

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

ASTRAL compendium enhancements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Fold change in evolution of protein 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=4171485

Ab initio protein structure prediction: progress and prospects.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Contemporary approaches to protein structure classification

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

CATH--a hierarchic classification of protein domain 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=4171485

Circular permutations of natural protein sequences: structural evidence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Structural trees for protein superfamilies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

The FSSP database of structurally aligned protein fold families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

SCOP: a structural classification of proteins database for the investigation of sequences and 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=4171485

Swaposins: circular permutations within genes encoding saposin homologues

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Why do globular proteins fit the limited set of folding patterns?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Structure of proteins: packing of alpha-helices and pleated sheets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4171485

Structural drift: a possible path to protein fold change

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0107959

Quantifying the similarities within fold space

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0107959

MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0107959

MALISAM: a database of structurally analogous motifs in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0107959

Are there knots in proteins?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0107959

A graph spectral analysis of the structural similarity network of protein chains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0107959

10.1371/JOURNAL.PONE.0107959

21 January 2018

Identifiers

DOI

1 reference

release_vr2x7eup7zbu5f6l5tmcnhfri4

13 October 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/vr2x7eup7zbu5f6l5tmcnhfri4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

13 October 2017

PubMed publication ID

25243952

1 reference