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MACiE specifications

Information


Unique identifier OMICS_02687
Name MACiE
Alternative name Mechanism, Annotation and Classification in Enzymes
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Gemma L. Holliday

Publication for Mechanism, Annotation and Classification in Enzymes

MACiE citations

 (17)
library_books

To what extent do structural changes in catalytic metal sites affect enzyme function?

2018
PMCID: 5760197
PMID: 29161638
DOI: 10.1016/j.jinorgbio.2017.11.002

[…] Enzyme Commission EG equistructural group a cluster with composition Fe7MoS9C that is the primary cofactor of nitrogenases guanosine triphosphate GYCH-I GTP cyclohydrolase I MACiE the database of Mechanism, Annotation and Classification in Enzymes the Metal-dependent subset of the MACiE database the Metal-binding subset of the Protein Data Bank Metal […]

call_split

Structure based prediction and identification of 4 epimerization activity of phosphate sugars in class II aldolases

2017
Sci Rep
PMCID: 5434028
PMID: 28512318
DOI: 10.1038/s41598-017-02211-3
call_split See protocol

[…] Structures were identified and classified using Protein Data Bank (PDB) and SCOPe. Information on reaction mechanisms was obtained from Mechanism, Annotation and Classification in Enzymes (MACiE). The similarity between single chain structures in each protein was calculated in PDB using the default flexible structure alignment by the FATCAT rigid algorithm. Amino acid sequence alignment […]

library_books

Biocuration in the structure–function linkage database: the anatomy of a superfamily

2017
PMCID: 5467563
PMID: 28365730
DOI: 10.1093/database/bax006

[…] proach (e.g. Pfam (), UniProtKB (), InterPro (), TIGRFAMs () and PANTHER () to name but a few), or a structure-centric approach [e.g. CATH () and SCOP ()] or a function-centric approach [e.g. CSA (), MACiE (), EzCatDB ()]. The SF approach integrates sequence, structure, and function as classification criteria, enhancing our abilities to discern new connections and features that help us better unde […]

library_books

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta Lactamases

2016
PLoS Comput Biol
PMCID: 4917113
PMID: 27332861
DOI: 10.1371/journal.pcbi.1004926

[…] nating the amide nitrogen atom [,].We assessed whether the FunFHMMer predictions of functional determinants (FDs) in the three classes captured the residue differences in the active sites reported in MACiE and the literature, and whether FunFHMMer could reveal additional sites distinguishing these classes. A three-way FunFam alignment was created by aligning the pooled sequences from each FunFam ( […]

library_books

Reaction Decoder Tool (RDT): extracting features from chemical reactions

2016
Bioinformatics
PMCID: 4920114
PMID: 27153692
DOI: 10.1093/bioinformatics/btw096

[…] Tools like EC-Blast (), FunTree (), MACiE () etc. use RDT in the background to mine and extract chemical information from thousands of enzyme reactions. The success rate of mapping is >99% when compared with manual AAM mappings (). Orig […]

library_books

Large Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies

2016
J Mol Biol
PMCID: 4751976
PMID: 26585402
DOI: 10.1016/j.jmb.2015.11.010

[…] Phylogenetic trees for 379 structurally defined enzyme superfamilies defined by the CATH classification were generated using the CSA and MACiE databases to help define enzyme containing CATH domain superfamilies. Using the improved protocol described above for producing structurally informed multiple sequence alignments, we generated […]

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MACiE institution(s)
EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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