(Q35643675)

9 August 2017

Inference of functional properties from large-scale analysis of enzyme superfamilies (English)

1 reference

9 August 2017

2

Patricia C Babbitt

1 reference

9 August 2017

Shoshana D Brown

1

1 reference

PubMed ID

22069325

9 August 2017

language of work or name

English

0 references

publication date

8 November 2011

1 reference

Journal of Biological Chemistry

9 August 2017

8

1 reference

based on heuristic

inferred from page(s)

published in

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9 August 2017

287

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9 August 2017

35-42

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9 August 2017

1

1 reference

PubMed ID

22069325

describes a project that uses

9 August 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

Divergent evolution in enolase superfamily: strategies for assigning functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

BRENDA, the enzyme information system in 2011

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Ongoing and future developments at the Universal Protein Resource

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Curators of the world unite: the International Society of Biocuration

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

A human gut microbial gene catalogue established by metagenomic sequencing

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Graphle: Interactive exploration of large, dense graphs

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Automatic policing of biochemical annotations using genomic correlations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

The Pfam protein families database

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Glutathione transferases are structural and functional outliers in the thioredoxin fold

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Protein function prediction--the power of multiplicity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Integration of biological networks and gene expression data using Cytoscape

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Automated protein subfamily identification and classification

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Evolution of function in the "two dinucleotide binding domains" flavoproteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Protein annotation at genomic scale: the current status

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Protein function space: viewing the limits or limited by our view?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Structural and functional diversity of the microbial kinome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Hierarchical classification of hydrolases catalytic sites

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Phylogenies of glutathione transferase families

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Structural evolution of the protein kinase-like superfamily

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Structural and catalytic diversity within the amidohydrolase superfamily

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

EzCatDB: the Enzyme Catalytic-mechanism Database

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Structures and mechanisms of Nudix hydrolases.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

CLANS: a Java application for visualizing protein families based on pairwise similarity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

The protein kinase complement of the human genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme a thioesters

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

Three protein kinase structures define a common motif

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3249087

An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations

27 July 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

BioLayout--an automatic graph layout algorithm for similarity visualization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

Nomenclature for mammalian soluble glutathione transferases

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

The evolution of function in strictosidine synthase-like proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

FAST: a novel protein structure alignment algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

Data Deposition and Annotation at the Worldwide Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R111.283408

21 January 2018

Identifiers

DOI

10.1074/JBC.R111.283408

1 reference

9 August 2017

1 reference

9 August 2017

1 reference

PubMed ID

22069325