RetroPath2.0
RetroPath2.0 is an automated open source workflow for retrosynthesis based on generalized reaction rules that perform the retrosynthesis search from chassis to target through an efficient and well-controlled protocol. Its easiness of use and the versatility of its applications make this tool a valuable addition to the biological engineer bench desk.
We show through several examples the application of the workflow to biotechnological relevant problems, including the identification of alternative biosynthetic routes through enzyme promiscuity or the development of biosensors. We demonstrate in that way the ability of the workflow to streamline retrosynthesis pathway design and its major role in reshaping the design, build, test and learn pipeline by driving the process toward the objective of optimizing bioproduction.
The RetroPath2.0 workflow is built using tools developed by the bioinformatics and cheminformatics community, because it is open source we anticipate community contributions will likely expand further the features of the workflow.
Basic Information
| Repository | https://github.com/brsynth/retropath2-wrapper |
| Documentation | https://github.com/brsynth/retropath2-wrapper |
| Seminar | Pablo Carbonell (I2SysBio-CSIC) presents the tools Selenzyme, DetSpace, RetroPath & Galaxy SynBioCAD |
| Main publication (DOI) | 10.1016/j.ymben.2017.12.002 view |
| Contact email | pablo.carbonell@csic.es |
| Authors/Maintainers | Pablo Carbonell |
| Type of application | Command line pipeline, Conda package, Galaxy tool |
| Programming languages | JavaPython |
| Keywords | Synthetic biology, Metabolic engineering, Retrosynthesis |
Technical details
| Input file formats | SMILES, InChI, CSV |
| Output file formats | CSV |
| Software compatibility | Linux, Mac, Windows |
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| Type of containerization | Conda |
| Wrapper type | None |
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| Citations (last 12 months) | <100 (~24 as of 15/10/2026) |
| Citations (since first release) | 100-1000 (247 as of 15/10/2026) |
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