Predicting metabolism

The Input

In order to predict metabolism, the BioTransformer Metabolism Prediction Tool (BMPT) accepts five parameters as input, described as follows:

  1. The task type (required): The user must select the “Metabolism Prediction” task.
  2. The BioTransformer option (required): The user can select one of the options depending of the aspect of metabolism that is of interest. The prediction could be specific (CYP450, Phase II, or EC-based), or comprehensive (Gut microbial, Environmental microbial, AllHuman, or Superbio). For a detailed explanation of the different option, please read the Overview page.
  3. The structure input (required): The input structures for starting compounds can be submitted in two different ways:
    1. A tab-separated text: Each line contains either a (preferably isomeric) SMILESstring, or a standard InChI of a starting compound. The structural representation (SMILES or standard InChI) can be preceded by an identifier (e.g. a name, a database ID).
    2. An SDF file: The SDF can be uploaded, and must contain the exact structure of each starting compound. For each starting compound, the optional identifier should be inserted in the header, just before the corresponding connection table. For more information, please consult the following document.
  4. The Number of iterations (optional): This determines the maximal number of biotransformation steps that will be predicted.
  5. The Submission title (optional): This allows the user to specify a title for the query. Please keep in mind that queries are accessible from the web server only through their query ID, as returned by BioTransformer.

The output

As default, the query output is returned in an HTML format that is displayed on the web interface. Users have the possibility to display results in a JSON or SDF format. Moreover, they can download the results in a single JSON, SDF, or CSV file.