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Prioritizing Compounds, Step 3: Predicting the Mutagenicity of the Selected Compounds

Predicting the Mutagenicity of the Selected Compounds

To add a further criterion to be used when selecting our drug candidates, we predict the compounds’ mutagenicities. To do so, we’ll use the ToxTree Benigni/Bossa rules for mutagenicity and carcinogenicity (Benigni et al., Mechanistic QSAR of aromatic amines: new models for discriminating between mutagens and nonmutagens, and validation of models for carcinogens, Environ Mol. Mutag. 48:754-771 (2007).). The URL of this model is

Analogously as you have done for the Cramer rules, navigate to the SuperService page in Ambit (, enter the dataset URI of the TCAMS dataset with the "?max=15000" appendix ( as well as the URI of the ToxTree Benigni/Bossa model ( to the appropriate fields and click "Run".

It is also possible to restrict calculations to the filtered list of the previous step only. In this case, use as the dataset URI.

OpenTox models store the prediction results (prediction features) again under data columns with a unique URI. These are available via http://host/model/{id}/predicted , which in our example corresponds to


The Toxtree Benigni/Bossa mutagenicity and carcinogenicity model predicts whether there are structural alerts for genotoxic or nongenotoxic carcinogenicity, and also uses a linear discriminant model for specific classes of compounds.

For our purpose, we select the columns “Structural Alert for genotoxic carcinogenicity“ ( and ”Structural Alert for nongenotoxic carcinogenicity“ ( As before, we add data columns for these structural alerts to our Cramer-class filtered list of compounds (use the URI from the previous step as a starting point), again using the feature_uris[] method. The resulting URL is:[]=[]=[]=[]=

In the following examples, we’ll consider the second compound in the image below as our antimalarial drug candidate. It is a Cramer class I compound that inhibits growth of P. falciparum 3D7 by 99% at the concentration tested (2µM), has a very low human cytotoxicity and no structural alerts for carcinogenicity. (You may choose a different compound).



Similarly to datasets and models, each compound in OpenTox services also has its unique URI. You can find the URI of a compound by clicking on its 2D structure, and stripping off the “?media=text/html” part at the end of the URI in the address bar of the browser. Alternatively, you can right-click the 2D drawing, select "Copy Link Location" (Firefox) or "Copy Shortcut" (Internet Explorer). When pasting the saved URI, again strip the “?media=text/html” part at the end of the URI.

The URL of the compound selected above is


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