Prioritizing Compounds, Step 2

Analyse Cytotoxicities of the Cramer Class I compounds
Analyse Cytotoxicities of the Cramer Class I compounds
Predicting the Mutagenicity

of the Selected Compounds

From the previous step we ended up with a list of compounds considered safe according to Cramer rules. The resulting table lists all the features of the compounds in the dataset. However, we would like to focus on the antimalarial activity and the human cytotoxicity only.

Cramer rules
(using the search URI http://apps.ideaconsult.net:8080/ambit2/dataset/584486?property=http://apps.ideaconsult.net:8080/ambit2/feature/22254&search=Low+(Class+I))

The TCAMS dataset contains antimalarial activity against two different strains of Plasmodium falciparum (the malaria-causing parasite): 3D7 and DD2. Antimalarial activity was measured as percentage growth-inhibition of the parasite at a compound concentration of 2 µM. The TCAMS dataset also contains growth inhibition data (at a compound concentration of 10 µM) of human hepatoma HepG2 cells, serving as an in vitro marker for liver toxicity.

To restrict the displayed columns, we need to edit the URI by adding an entry denoting the feature URIs of the antimalarial activity and the human cytotoxicity given in the TCAMS Dataset. To obtain the feature URIs, put your mouse pointer on the column title you are interested in, and not the feature URI at the bottom of your browser window. The antimalarial activity is the feature entitled "Percentage inhibition 3D7", and the human cytotoxicity is the feature "Percentage inhibition HepG2".

The two feature URIs are
http://apps.ideaconsult.net:8080/ambit2/feature/636441 for the "Percentage inhibition 3D7", and
http://apps.ideaconsult.net:8080/ambit2/feature/636442 for the "Percentage inhibition HepG2".

To restrict our filtered list of compounds considered safe according to Cramer rules (Cramer Class I) to these columns, we simply add a feature_uris[] parameter to the URI of our filtered list:
http://apps.ideaconsult.net:8080/ambit2/dataset/584486?property=http://a...(Class+I)&feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/636441&feature_uris[]=ht...

Copy this address into the web browser and browse the results.

PROCEED TO STEP 3:

Predicting the Mutagenicity of the Selected Compounds

STEPS:
Step 1: Predicting Oral Toxicity
Step 2: Analyse Cytotoxicities of the Cramer Class I compounds
Step 3: Predicting the Mutagenicity of the Selected Compounds
Step 4: Predicting Sites of Cytochrome P450 Metabolism

BACK TO Drug Discovery Predictive Toxicology Tutorial Overview