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. CYP450 metabolism plays a very important role in drug metabolism and ususally increase the water solubility of the substrate.
- EC-Based: Select this option for the prediction of promiscuous metabolism (e.g. glycerolipid metabolism). EC-based metabolism is also called Enzyme Commission based metabolism. It generates metabolites using reaction rules associated with different enzymes specified by enzyme commission numbers.
- 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. It collects the enzymes live in organs in human gut and generate metabolites using the corresponding reactions.
- 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. It runs AllHuman for 4 iterations in our current version.
- MultiBio: Select this option to create your own biotransformation sequence by any combination of CYP450, PhaseII, EC-Based, Gut Microbial and Enviromental metabolism with different number of iterations.
- AbioticBio: Select this option to predict abiotic biotransformation including photochemical, chlorination, ozonation reactions.
Please note that it may take much longer to make predictions when select more number of steps.
This parameter is only useful when CYP450, AllHuman or SuperBio is selected. It's also used when the user selects CYP450 in any step in the MultiBio module.
Rule Based: CYP450 module will use the rule-based method to generate metabolites.
CyProduct: CYP450 module will use the machine-learned tool CyProduct to make predictions for CYP450 metabolism.
Combined: CYP450 module will use both the rule-based method and the machine-learned model and combine the results together.