Retrosynthesis is a long-standing problem first introduced by Chemistry Nobel Laureate J.E. Corey in the late 1960s. Taking advantage of recent progresses made in machine learning the problem has been revisited. In two papers SYNBIOCHEM teamed up with MICALIS Institute at INRA (France) to explore the use of retrosynthesis in biology. Both articles are making use of RetroPath2.0 a versatile, open source, easy to use and modifiable scientific workflow. In the first paper [1] the tool is used to perform retrosynthesis in the context of metabolic and biosensor engineering and is validated using actual examples of successful experimental implementations. In the second paper [2] the tool is used to perform inverse molecular design and search bioactive molecules in the chemical space as well as to create extended metabolic maps that can be used to annotate mass spectrometry data coming from a metabolomics pipeline. Because RetroPath2.0 is freely available on the workflow repository platform myExperiment.org [3] and is solely based on open source tools it is anticipated that community contributions will likely expand further its features.
[1] Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering 2017, https://doi.org/10.1016/j.ymben.2017.12.002
[2] Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. J. Cheminformatics 2017, in press https://doi.org/10.1101/158147
[3] RetroPath2.0 download page: https://www.myexperiment.org/workflows/4987.html