Tool stats & trends
Looking to identify usage trends or leading experts?
|Alternative name||Mechanism, Annotation and Classification in Enzymes|
|Restrictions to use||None|
- person_outline Gemma L. Holliday
Publication for Mechanism, Annotation and Classification in Enzymes
To what extent do structural changes in catalytic metal sites affect enzyme function?
[…] 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 […]
Structure based prediction and identification of 4 epimerization activity of phosphate sugars in class II aldolases
[…] 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 […]
Biocuration in the structure–function linkage database: the anatomy of a superfamily
[…] 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 […]
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta Lactamases
[…] 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 ( […]
Reaction Decoder Tool (RDT): extracting features from chemical reactions
[…] 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 […]
Large Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies
[…] 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 […]
Looking to check out a full list of citations?
Be the first to review MACiE