EC-BLAST statistics

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EC-BLAST specifications

Information


Unique identifier OMICS_20284
Name EC-BLAST
Interface Web user interface
Restrictions to use None
Input data EC Number or reaction name or a molecule name or a molecule file.
Input format MDL V2
Output data The mapping with best chemical outcome.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Janet Thornton <>

Additional information


http://www.ebi.ac.uk/thornton-srv/software/rbl/faq.html

Publication for EC-BLAST

EC-BLAST in publications

 (6)
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] biologically incorrect predictions (i.e., subsequent reaction steps may use different stereoisomers). however, stereochemical changes have already been captured by many computational tools such as ec-blast and reaction decoder tool , which use the chemistry development kit (cdk) , and clca to model stereochemical changes by appending stereochemical descriptors to the canonical labeling […]

PMCID: 5042172
PMID: 27924274
DOI: 10.2142/biophysico.13.0_195

[…] based not on amino acid sequence similarity but on chemical structure similarity. several other methods to predict ec numbers from chemical structures have been subsequently developed [–], including ec-blast [], which allows one to search for enzymatic reactions with ec numbers that are similar to the query reaction based on bond-change, reaction-center, or reaction-structure similarity., enzyme […]

PMCID: 4740462
PMID: 26840640
DOI: 10.1371/journal.pone.0147952

[…] attributes from biochemical reactions such as bond changes is necessary to compare enzymes based on the chemistry of their catalysed reactions. in order to calculate chemical attributes we used ec-blast, a recently-developed algorithm to obtain accurate atom-atom mapping, extract bond changes and perform similarity searches between enzyme reactions []., to study reaction diversity across […]

PMCID: 4751976
PMID: 26585402
DOI: 10.1016/j.jmb.2015.11.010

[…] within the same fold group., though the ec numbering system is good for curating enzyme functions, it is not useful for making quantitative comparisons between reaction chemistries. by using ec-blast, we can quantify the functional changes observed in the ec exchange matrix by calculating similarities in bond order changes, reaction centres, and substrate/product sub-structures (). […]

PMCID: 4139412
PMID: 25000289
DOI: 10.1016/j.sbi.2014.06.002

[…] are comparatively analysed using functional and all-against-all sequence similarity., to explore the evolution of the isomerases, we have calculated the functional similarity between enzymes using ec-blast [], a recently developed algorithm to automatically compare biochemical reactions. this approach introduces three measures of functional similarity — comparison of bond changes, reaction […]


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EC-BLAST institution(s)
European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK ; European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK ; European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, London, UK; European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
EC-BLAST funding source(s)
Supported by the EMBL. NF is funded by the Wellcome Trust (Grant No.081989/Z/07/A).

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