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Protocols

ENZYME specifications

Information


Unique identifier OMICS_02682
Name ENZYME
Alternative name Enzyme nomenclature database
Restrictions to use None
Maintained Yes

Additional information


Manual: http://enzyme.expasy.org/enzuser.txt

Publication for Enzyme nomenclature database

ENZYME citations

 (6)
library_books

AFAL: a web service for profiling amino acids surrounding ligands in proteins

2014
J Comput Aided Mol Des
PMCID: 4241235
PMID: 25085083
DOI: 10.1007/s10822-014-9783-6

[…] AFAL has been compiled using pre-existing and publically available resources and software packages (Fig. ) such as the PDB database [–], its Ligand Expo Search feature [], the IUBMB Enzyme Nomenclature Database [], the NCBI Taxonomy Database [] and the VMD software []. The AFAL web service consists of three major components, the AFAL Database, the Consultation web interface and t […]

library_books

The Complete Genome Sequence of the Plant Growth Promoting Bacterium Pseudomonas sp. UW4

2013
PLoS One
PMCID: 3596284
PMID: 23516524
DOI: 10.1371/journal.pone.0058640

[…] COG was searched against the NCBI COG database – and an E.C. number was assigned by PRIAM . The results from both pipelines were compared and manually corrected based on the current COG database and Enzyme nomenclature database . Protein localization was predicted by PSORTb v3.0.2 and genomic islands (GIs) were detected using IslandViewer . Repeat sequences were examined by Tandem Repeats Finder […]

library_books

iPathCaseKEGG: An iPad interface for KEGG metabolic pathways

2013
PMCID: 4336120
PMID: 25825656
DOI: 10.1186/2047-2501-1-4

[…] n is shown on the left hand side.Figure 2Figure 3Figure 4Figure 5Figure 6Figure 7Figure 8In addition to displaying a node’s long description from PathCaseKEGG, iPathCaseKEGG uses data from the ENZYME enzyme nomenclature database [] to show more information for reactions for which EC numbers are available. ENZYME’s data comes from the recommendations of the Nomenclature Committee of the Internation […]

library_books

MESSA: MEta Server for protein Sequence Analysis

2012
BMC Biol
PMCID: 3519821
PMID: 23031578
DOI: 10.1186/1741-7007-10-82

[…] [,]. For the first approach, the closely related Swiss-Prot entries and their assigned EC numbers are shown, while for the other two approaches, the predicted EC numbers and their definitions in the ENZYME nomenclature database [] are listed. […]

call_split

Evolutionary Innovations and the Organization of Protein Functions in Genotype Space

2010
PLoS One
PMCID: 2994758
PMID: 21152394
DOI: 10.1371/journal.pone.0014172
call_split See protocol

[…] ercent, thus obtaining a dataset of 136,677 sequences. We discarded sequences tagged with any of the keywords: “putative”, “probable”, “by homology”. As a source of functional annotation, we used the Enzyme Nomenclature Database (EC) . Since the EC classification distinguishes four different hierarchical levels of enzyme function, we used only EC assignations that possess numerical descriptors for […]

library_books

Reconstruction and analysis of genome scale metabolic model of a photosynthetic bacterium

2010
BMC Syst Biol
PMCID: 3009638
PMID: 21083885
DOI: 10.1186/1752-0509-4-156

[…] ins and metabolites presents in the organism. The list of reactions was then retrieved from Pathway Tools; EC numbers and stoichiometry of the reactions were checked and verified with the help of the Enzyme nomenclature database [] and KEGG pathway database []. Reactions were elementally balanced except for protons, so that chemical conversions were coherent. In some of the reactions present in th […]


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ENZYME institution(s)
Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland

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