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Publications for Rhea
A review of computational tools for design and reconstruction of metabolic pathways
[…] to constitute the pathway of interest. Currently, a number of databases have been constructed for known biochemical reactions and pathways (i.e., BIGG , KEGG , MetaCyc , BRENDA , ModelSEED , MetRxn , Rhea , UM-BBD , MOS , and Beilste Crossfile ), as well as hypothetical metabolites and reactions (such as ATLAS of Biochemistry , and MINE ) (see A). The current version of BIGG database consists of 8 […]
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis
[…] trates and products may be listed exhaustively in the Enzyme List. Third, spontaneous reactions are not present in the Enzyme List.Many reaction databases (such as BRENDA , KEGG , MetaCyc , and Rhea ) use the Enzyme List to reconstruct metabolic pathways and supplement with additional reactions to fill in the gaps. These reconstructed pathways can be represented as combined pathways that o […]
Reaction Decoder Tool (RDT): extracting features from chemical reactions
[…] Large-scale chemical reaction databases such as KEGG (), BRENDA (), Rhea () and MetaCyc () link reactions to enzymes and provide data-mining opportunities for novel pathways (; ), and the discovery of drugs, natural products and green chemistry. One of the primary bot […]
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases
[…] reference for the hierarchical enzymatic classification of the IUBMB/IUPAC joint nomenclature committee that is maintained by SIB. Explicit representations of enzymatic reactions are also provided by Rhea (www.ebi.ac.uk/rhea), a comprehensive and non-redundant resource of expert-curated biochemical reactions () described using species from the ChEBI (Chemical Entities of Biological Interest) ontol […]
The EBI enzyme portal
[…] We used Java technologies—Spring Web MVC, JAXB, JAX-WS—and several Web Service APIs either SOAP—EB-Eye, ChEBI, CiteXplore—or REST—UniProt, Reactome, Rhea, ChEMBL, BioMart, DAS—to build the web application. XML schemas describe the underlying model.For quick cross-referencing and building filters for search results, an Oracle database was populated […]
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