Global view of the protein universe (Q34060564)

30 July 2017

title

Global view of the protein universe (English)

1 reference

30 July 2017

Nir Ben-Tal

2

0 references

Rachel Kolodny

series ordinal

3

object named as

Rachel Kolodny

1 reference

30 July 2017

Sergey Nepomnyachiy

1

1 reference

30 July 2017

language of work or name

English

0 references

publication date

28 July 2014

1 reference

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

30 July 2017

number of pages

6

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

30 July 2017

volume

111

1 reference

30 July 2017

issue

32

1 reference

30 July 2017

page(s)

11691-11696

1 reference

describes a project that uses

30 July 2017

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

cites work

A travel guide to Cytoscape plugins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Evolution of protein domain architectures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Maps of protein structure space reveal a fundamental relationship between protein structure and function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Touring protein space with Matt

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

On the evolutionary origins of "Fold Space Continuity": a study of topological convergence and divergence in mixed alpha-beta domains.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

The continuity of protein structure space is an intrinsic property of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Discrete-continuous duality of protein structure space.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Nothing about protein structure classification makes sense except in the light of evolution.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Is protein classification necessary? Toward alternative approaches to function annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Evolution of protein domain promiscuity in eukaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Probing protein fold space with a simplified model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Evolutionary transitions in protein fold space

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

SISYPHUS--structural alignments for proteins with non-trivial relationships

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Evolution of protein structural classes and protein sequence families.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

More than the sum of their parts: on the evolution of proteins from peptides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Evolution of the protein repertoire

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Expanding protein universe and its origin from the biological Big Bang

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

The natural history of protein domains

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Protein structure prediction and structural genomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

An alternative view of protein fold space

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

The ASTRAL compendium for protein structure and sequence analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

5 July 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

CATH--a hierarchic classification of protein domain structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Mapping the protein universe

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Structural patterns in globular proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

On the universe of protein folds

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1403395111

Quantifying the similarities within fold space

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1403395111

Scale-free behavior in protein domain networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1403395111

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1403395111

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4136566

Proteins with class alpha/beta fold have high-level participation in fusion events

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25071170

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1403395111

1 reference

30 July 2017

0 references

1 reference

30 July 2017

1 reference