Enzyme Databases in the Era of Omics and Artificial Intelligence
Abstract
:1. Introduction
1.1. Enzyme Classification
1.2. Enzyme Databases
2. The Quest to Standardize Data Reporting
3. The Future of Enzyme Databases in the Light of Recent Artificial Intelligence Developments
4. Overview of General Enzyme Databases
4.1. Enzyme Nomenclature Databases: ExplorEnz, IntEnz, and ExPASy ENZYME
4.2. BRENDA
4.3. SABIO-RK
4.4. Reaction Mechanism Databases: M-CSA and EzCatDB
4.5. MetaCyc
4.6. KEGG
4.7. Reactome
4.8. GotEnzymes
4.9. TopEnzyme
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Database Type | Database | Scope of Database | Data Source | Curation |
---|---|---|---|---|
Enzyme nomenclature | ExplorEnz | IUBMB classification [12] | IUBMB enzyme list | Manual |
ExPASy ENZYME | IUBMB classification with references to UniProt entries [13] | IUBMB enzyme list | Manual | |
IntEnz | IUBMB classification with references to UniProt and ChEBI entries [14] | IUBMB enzyme list | Manual | |
Kinetics | BRENDA | Function and kinetic parameters, enzyme–ligand interactions, organism-related information, isolation methods [15] | Experimental (implementation of some prediction tools) | Manual and automated * |
SABIO-RK | Kinetic parameters with experimental conditions [16] | Experimental | Manual (option of data submission by experimenters) | |
STRENDA-DB | Standardized kinetic data [17] | Experimental | Submission of data by experimenters | |
IntEnzyDB | A comparison of kinetic parameters between wildtype and mutant enzymes [18] | Integration from multiple databases | Automated | |
D3DistalMutation | Effects of mutations on enzyme activity [19] | Integration from multiple databases | Automated (mostly) | |
GotEnzymes | Kinetic parameters predicted with a computer algorithm [20] | Predicted | Automated | |
Structure | UniProt | Protein sequence and functional information [3] | Experimental and predicted | Manual and automated |
PDB ** | Experimentally verified protein structures [21] | Experimental | Manual | |
AlphaFold DB ** | Protein structures predicted with a computer algorithm [22] | Predicted | Automated | |
TopEnzyme | Enzyme structures predicted with a computer algorithm [23] | Predicted | Automated | |
Ligand-induced domain movements in enzymes | Data on movements of enzyme domains upon ligand binding [24] | Experimental | Manual and automated | |
CoFactor | Data on organic enzyme cofactors [25] | Experimental | Manual and automated | |
Natural Ligand DataBase | Structural data on enzyme–ligand interactions [26] | Experimental and predicted | Automated | |
Phylogeny | FunTree | Sequence, structural, and phylogenetic data on enzymes and other proteins fun [27] | Integration from multiple databases | Automated |
Reactions (general) | ATLAS of Biochemistry | A database of all theoretical biochemical reactions [28] | Experimental and predicted | Automated |
BKMS-react | List of biochemical reactions from BRENDA, KEGG, MetaCyc, and SABIO-RK [29] | Integration from multiple databases | Automated | |
EnzyMine | Mining of enzymatic reactions linked to sequence and structural annotations [30] | Integration from multiple databases | Manual | |
Rhea | A resource of biochemical reactions [31] | IUBMB enzyme list | Manual | |
Reaction explorer | Biochemical reactions derived from IUBMB enzyme list [32] | IUBMB enzyme list | Manual | |
Reaction mechanism | M-CSA | Information on position and role of catalytic residues and annotated step-by-step reaction mechanisms [33] | Experimental | Manual |
EzCatDB | A hierarchical classification of catalytic mechanisms [34] | Experimental | Manual | |
Metabolic pathways | KEGG | Information about metabolic pathways, reactions, metabolites, enzymes, and genes [35] | Experimental | Manual |
MetaCyc | Information about metabolic pathways, reactions, metabolites, enzymes, and genes [36] | Experimental | Manual | |
PathBank | A metabolic pathway resource for model organisms [37] | Experimental | Manual | |
Reactome | Information about biological pathways in human and model organisms [38] | Experimental | Manual and automated | |
Secondary information resource | Enzyme Portal | Integration of publicly available enzyme information [10] | Integration from multiple databases | Automated |
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Prešern, U.; Goličnik, M. Enzyme Databases in the Era of Omics and Artificial Intelligence. Int. J. Mol. Sci. 2023, 24, 16918. https://doi.org/10.3390/ijms242316918
Prešern U, Goličnik M. Enzyme Databases in the Era of Omics and Artificial Intelligence. International Journal of Molecular Sciences. 2023; 24(23):16918. https://doi.org/10.3390/ijms242316918
Chicago/Turabian StylePrešern, Uroš, and Marko Goličnik. 2023. "Enzyme Databases in the Era of Omics and Artificial Intelligence" International Journal of Molecular Sciences 24, no. 23: 16918. https://doi.org/10.3390/ijms242316918