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MetaRoute specifications


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


Pathway design using de novo steps through uncharted biochemical spaces

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 […]


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

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 […]


A review of parameters and heuristics for guiding metabolic pathfinding

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 […]


A Method for Finding Metabolic Pathways Using Atomic Group Tracking

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 […]


CMPF: Class switching minimized pathfinding in metabolic networks

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 […]


Inferring branching pathways in genome scale metabolic networks

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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