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MetaRoute specifications

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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 citations

 (6)
library_books

Pathway design using de novo steps through uncharted biochemical spaces

2018
Nat Commun
PMCID: 5766603
PMID: 29330441
DOI: 10.1038/s41467-017-02362-x

[…] ymatic 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 c […]

library_books

A review of computational tools for design and reconstruction of metabolic pathways

2017
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] athway 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 the i […]

library_books

A review of parameters and heuristics for guiding metabolic pathfinding

2017
J Cheminform
PMCID: 5602787
PMID: 29086092
DOI: 10.1186/s13321-017-0239-6

[…] veral 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 […]

library_books

A Method for Finding Metabolic Pathways Using Atomic Group Tracking

2017
PLoS One
PMCID: 5221824
PMID: 28068354
DOI: 10.1371/journal.pone.0168725

[…] get 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 atoms […]

library_books

CMPF: Class switching minimized pathfinding in metabolic networks

2012
BMC Bioinformatics
PMCID: 3521384
PMID: 23282238
DOI: 10.1186/1471-2105-13-S17-S17

[…] We compare CMPF using standard reference metabolic pathways as defined in [] against MRSD [], MetaRoute [] and a pathfinding method in the NEAT software package described in []. MRSD and MetaRoute use compound transform graph to model the metabolic network and use species support and node conn […]

library_books

Inferring branching pathways in genome scale metabolic networks

2009
BMC Syst Biol
PMCID: 2791103
PMID: 19874610
DOI: 10.1186/1752-0509-3-103

[…] ethod by adding a support for branching pathways. Moreover, our method is a generalization of the ARM method as we can simulate ARM by setting ReTrace to find unbranched pathways only. In contrast to MetaRoute [] and Metabolic Pathfinding [], ReTrace finds paths in the atom-level metabolic network, instead of using the indirect method of encoding metabolite similarity into graph weights. This allo […]


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

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