RetroPath statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RetroPath
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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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Versioning


No version available

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 citations

 (13)
library_books

Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms

2018
Front Microbiol
PMCID: 5816047
PMID: 29483901
DOI: 10.3389/fmicb.2018.00155

[…] nthesis approach, which is a well-established method used in organic chemistry for identifying suitable precursors and synthesis routes, was combined with biological knowledge to create tools such as RetroPath () to automate the pathway design process. Several possible pathways consisting of various enzymes that can lead precursors to the target compound can be proposed and ranked based on selecte […]

library_books

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

2017
J Cheminform
PMCID: 5736515
PMID: 29260340
DOI: 10.1186/s13321-017-0252-9

[…] In this section we used RetroPath2.0 to search all molecules that are at predefined distances of a given set of molecules. Such queries are routinely carried out in large chemical databases for drug discovery purposes [], bu […]

library_books

Production of C2–C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies

2017
Biotechnol Biofuels
PMCID: 5727944
PMID: 29255482
DOI: 10.1186/s13068-017-0992-9

[…] matics, different algorithms and prediction tools have been developed to aid in in silico pathway design and metabolic engineering [–]. Especially, several pathway prediction tools, such as BNICE and RetroPath which consider also promiscuous enzyme reactions, can be used for prediction and prioritization of various possible pathways to a given compound [, ]. In these computational frameworks, a ch […]

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

[…] r 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 unli […]

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

[…] FMM [], reactions are represented as a 16,884×16,884 matrix, where each row and column represents a compound and having a ‘1’ represents that there exists a forward reaction between the compounds. In RetroPath by Carbonell et al. [], the molecular signature of any given compound is defined by a subset of neighboring atoms and chemical bonds surrounding each individual atom in the compound. The rea […]

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

[…] iotechnological 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 of the reactions […]


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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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