Nothing about protein structure classification makes sense except in the light of evolution. (Q30376508)

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Language	Label	Description	Also known as
English	Nothing about protein structure classification makes sense except in the light of evolution.	scientific article

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

1 reference

Europe PubMed Central

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

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

protein evolution

0 references

3

object named as

Philip E Bourne

0 references

1

object named as

Ruben E Valas

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

author name string

Song Yang

2

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

publication date

24 April 2009

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

Current Opinion in Structural Biology

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

19

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

3

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

329-334

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

The evolutionary history of protein domains viewed by species phylogeny

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Arrangements in the modular evolution of proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Assembly reflects evolution of protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The structure of protein evolution and the evolution of protein structure.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Evolution of protein domain promiscuity in eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Characters of very ancient proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Gene3D: comprehensive structural and functional annotation of genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

From protein sequence space to elementary protein modules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The design and characterization of two proteins with 88% sequence identity but different structure and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Evolutionary history and functional implications of protein domains and their combinations in eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Evolutionary transitions in protein fold space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Pattern pluralism and the Tree of Life hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The generation of new protein functions by the combination of domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Modeling the evolution of protein domain architectures using maximum parsimony

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

3D complex: a structural classification of protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The SUPERFAMILY database in 2007: families and functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Cognate Ligand Domain Mapping for Enzymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Protein superfamily evolution and the last universal common ancestor (LUCA).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Partitioning protein structures into domains: why is it so difficult?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Rooting the tree of life by transition analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Protein family expansions and biological complexity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Evolution of protein fold in the presence of functional constraints

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Fragnostic: walking through protein structure space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Evolutionary aspects of whole-genome biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

PROTEIN FAMILIES AND THEIR EVOLUTION—A STRUCTURAL PERSPECTIVE

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Toward consistent assignment of structural domains in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Supra-domains: evolutionary units larger than single protein domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Structure, function and evolution of multidomain proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Evolution of the protein repertoire

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The structure of the protein universe and genome evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Expanding protein universe and its origin from the biological Big Bang

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Birth and death of protein domains: a simple model of evolution explains power law behavior

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Critical issues in bacterial phylogeny

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Protein domain analysis in the era of complete genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Fold change in evolution of protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

An alternative view of protein fold space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Closed loops of nearly standard size: common basic element of protein structure.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 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=2696554

20 June 2018

A systematic comparison of protein structure classifications: SCOP, CATH and FSSP

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Distribution of protein folds in the three superkingdoms of life.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

Dali/FSSP classification of three-dimensional protein folds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The structural alignment between two proteins: is there a unique answer?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The multiplicity of domains in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The Protein Data Bank: a computer-based archival file for macromolecular structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

20 June 2018

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

26 November 2018

Using Dali for structural comparison of proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

26 November 2018

Quantification of the Elevated Rate of Domain Rearrangements in Metazoa

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

26 November 2018

A comparison of SCOP and CATH with respect to domain-domain interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

26 November 2018

Relative rates of gene fusion and fission in multi-domain proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

26 November 2018

Evolution of protein superfamilies and bacterial genome size

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

26 November 2018

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2696554

26 November 2018

Protein modules conserved since LUCA

1 reference

https://pubmed.ncbi.nlm.nih.gov/19394812

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The origin of genes could be polyphyletic

1 reference

https://pubmed.ncbi.nlm.nih.gov/19394812

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1016/J.SBI.2009.03.011

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

19 August 2017

ResearchGate publication ID

0 references

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