RetroPath statistics

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RetroPath specifications

Information


Unique identifier OMICS_20278
Name RetroPath
Alternative name RetroPath2.0
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainers


  • person_outline Thomas Duigou <>
  • person_outline Jean-Loup Faulon <>

Additional information


https://www.myexperiment.org/workflows/4987.html https://github.com/brsynth/rp2paths

Information


Unique identifier OMICS_20278
Name RetroPath
Alternative name RetroPath2.0
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A first set of compounds (the source), a second set of compounds (the sink) and a set of reaction rules.
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
Knime Analytics Platform
Maintained Yes

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Maintainers


  • person_outline Thomas Duigou <>
  • person_outline Jean-Loup Faulon <>

Additional information


https://www.myexperiment.org/workflows/4987.html https://github.com/brsynth/rp2paths

Publications for RetroPath

RetroPath in publications

 (10)
PMCID: 5736515
PMID: 29260340
DOI: 10.1186/s13321-017-0252-9

[…] the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for., here, we showcase the use of the open source workflow retropath2.0. first, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. we then use this enumeration strategy to screen […]

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

[…] exhaustive pathway exploration. for example, the initial bnice computational framework generates an exponentially growing range of hypothetical molecules . in order to reduce the search space, xtms/retropath uses a diameter which defines graph distance of atoms within the radius to control the network size , . um-pps applies reactions rules based on an ‘absolute aerobic likelihood’ to prune […]

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

[…] the data stored in curated metabolic databases. other databases like atlas [] and xtms [] store information on extended search spaces and even apply existing pathfinding techniques (bnice [, ] and retropath [], respectively) to these spaces. metabolic pathfinding may not be the main focus of retrosynthesis algorithms and expanded databases; however, these resources are nevertheless critical […]

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

[…] analysis of pathways to increase the yield of important metabolites []. a number of the stoichiometric methods, such as cfp [–], pathtracer [], optstrain [], optstoic [], ncga [], and retropath [], has been proposed., graph-based pathfinding methods find possible metabolic pathways converting a given start compound to a given target compound through the connectivity […]

PMCID: 5625740
PMID: 29062953
DOI: 10.1016/j.synbio.2016.07.001

[…] this work builds on our strong foundation in the development of genome mining tools, such as antismash , and automated pipelines for cheminformatics and biosynthetic pathway prediction, such as retropath and related tools , , , . the recent development of sensipath, for the enhanced design of metabolic pathways with intermediates that are detectable by biosensors and therefore amenable […]


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RetroPath institution(s)
CNRS-UMR8030 / Laboratoire iSSB, Université Paris-Saclay, Evry, France; CEA, DRF, IG, Genoscope, Evry, France; Micalis Institute, INRA, AgroParisTech, Universite Paris-Saclay, Jouy-en-Josas, France; SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
RetroPath funding source(s)
Supported by the French National Research Agency [ANR-15-CE1-0008], the Biotechnology and Biological Sciences Research Council, Centre for synthetic biology of fine and speciality chemicals [BB/M017702/1], Synthetic Biology Applications for Protective Materials [EP/N025504/1], and GIP Genopole.

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