BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. Moreover, it can also assist scientists in the identification of metabolites, which is based on the metabolism prediction. BioTransformer uses both a knowledge-based approach and a machine learning based approach to predict small molecules metabolism. In particular, BioTransformer consists of five independent modules: EC-based, CYP450, Phase II, Human Gut Microbial and Environmental Microbial. The BioTransformer library is available at this Bitbucket page.
- Djoumbou Feunang Y, Fiamoncini J, de la Fuente AG, Manach C, Greiner R, and Wishart DS; BioTransformer: A Comprehensive Computational Tool for Small Molecule Metabolism Prediction and Metabolite Identification; Journal of Cheminformatics; 2019; Journal of Cheminformatics 11:2; DOI: 10.1186/s13321-018-0324-5
Selecting a Task
Select Metabolism Prediction to predict metabolic transformations given a starting compound, or Metabolite Identification to identify putative metabolites of a starting molecule that match a given set of masses or molecular formulas
Selecting a Metabolic Transformation
Select between seven different options for the prediction or identification. Five options allow for a specific coverage metabolism, and include the CYP450, EC-Based, Phase II, Gut microbial, and Environmental microbial options. Two options allow for a comprehensive coverage of metabolism in the human superorganism, and include the allHuman, and superbio options.
- CYP450: Select this option for CYP450 metabolism prediction.
- EC-Based: Select this option for the prediction of promiscuous metabolism (e.g. glycerolipid metabolism).
- Phase II: Select this option for the prediction of major conjugative reactions, including glucuronidation, sulfation, glycine transfer, N-acetyl transfer, and glutathione transfer, among others.
- Gut microbial: Select this option to predict xenobiotic metabolism by gut microbial enzymes
- Environmental microbial: Select this option to predict or identify products of the environmental microbial degradation of small organic molecules
- AllHuman: Select this option to predict or identify products of small molecule metabolism in the human superorganism. This covers biotransformations occurring both in human tissues as well as well as the gut microbiota. Each step of the metabolism prediction/metabolite identification covers human as well as gut microbial transformations, when applicable.
- Superbio: Select this option to predict or identify products of small molecule metabolism in the human superorganism. This covers biotransformations occurring both in human tissues as well as well as the gut microbiota. In contrast to the allHuman option, BioTransformer follows a defined sequence of reaction types, starting from promiscuous metabolic reactions alone, followed by CYP450-catalyzed reactions, gut microbial degradation, and Phase II reactions.