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MetaRoute specifications

Information


Unique identifier OMICS_03568
Name MetaRoute
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for MetaRoute

MetaRoute in publications

 (5)
PMCID: 5766603
PMID: 29330441
DOI: 10.1038/s41467-017-02362-x

[…] functions to assemble pathways toward targeted chemicals. this is an area of research with significant prior work. network-based path finding methods such as pathcomp, pathway hunter tool, and metaroute identify linear pathways from a single source to one target molecule. these methods rely on heuristics such as substrate-product similarity, atom transitions, or substrate-product reaction […]

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

[…] would entail the use of a more comprehensive database encompassing multiple organisms, thereby ensuring that a desirable biotransformation (i.e., gene/enzyme) can be found (e.g., optstoic and metaroute use the curated kegg database; xtms uses metacyc)., the potential of broad-substrate enzymes or synthetic enzymes to catalyze previously unknown or de novo reactions have also garnered […]

PMCID: 5602787
PMID: 29086092
DOI: 10.1186/s13321-017-0239-6

[…] earlier pathfinding algorithms [–]. it is also possible for the nodes in a metabolic graph to represent the enzymatic reactions and the edges to represent the intermediate compounds, as done in metaroute []. another possible graph representation of the metabolic network is for both compounds and reactions to be represented as nodes in a bipartite graph, where edges represent the connections […]

PMCID: 5221824
PMID: 28068354
DOI: 10.1371/journal.pone.0168725

[…] compounds, their experimental results showed that atom tracking significantly improves the performance of metabolic pathfinding. different from the methods using atom mapping data from databases, metaroute [, ] automatically computes atom mapping rules based on enzyme ec numbers and compound smiles, and uses the computed atom mapping data to avoid finding pathways that lose all conserved […]

PMCID: 2791103
PMID: 19874610
DOI: 10.1186/1752-0509-3-103

[…] had been found between the query metabolites, a check would be made to ensure that at least one atom is actually transferred from source to target. the method has been implemented as the tool metaroute []., subsequently, also metabolic pathfinding was improved by faust et al. by taking advantage of the annotations for reactant pairs in kegg reactions contained in the rpair database []. […]


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MetaRoute institution(s)
Division for Simulation of Biological Systems, ZBIT/WSI, University of Tübingen, Tübingen, Germany

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