How to Use Toxtree to Determine Cramer Class and Estimate Toxic Hazard

Little Pro on 2018-04-04

Toxtree is a free QSAR tool that can be used to determine the Cramer class of a chemical substance and estimate its relative toxic hazard. It is jointly developed by Ideaconsult Ltd (Sofia, Bulgaria) and the Join Research Centre (JRC) of the European Commission. In this article, we will show you how to use Toxtree step by step.

Introduction to Cramer Class

The Cramer classification scheme (decision tree) is the best known approach to estimate the Threshold of Toxicological Concern  (TTC) for a chemical substance based on its chemical structure. There are three Cramer classes whith class III representing the most severe toxic hazard. Class III chemical compounds are assigned with the lowest TTC values.

Cramer Class Description TTC (µg/day*)
I Substances of simple chemical structure with known metabolic pathways and innocuous end products which suggest a low order of oral toxicity. 1,800 (30 µg/kg bw/d)
II Substances that are intermediate. They possess structures that are less innocuous than those in Class 1 but they do not contain structural features that are suggestive of toxicity like those in Class 3. 540 (9 µg/kg bw/d)
III Substances with chemical structures that permit no strong initial impression of safety and may even suggest a significant toxicity. 90 (1.5 µg/kg bw/d)

How to Use Toxtree

Step 1: Download and Install

Toxtree can be downloaded here. It only works on Windows operation system. It is very easy to install.

Step 2: Create A New Molecule

Click "File" -> "New molecule"

Toxtree Molecule

Step 3: Edit Compounds

Click "Chemical compounds" -> "Edit compounds". 

Toxtree edit compounds

A new editor window will then pop up. You can either draw chemical structure or enter SMILES code. SMILES (Simplified Molecular Input Line Entry System) is a molecular text code of displayed chemical STRUCTURE. 

SMILES is required as input by many QSAR models. For a big majority of chemical substances, you may find SMILES via the links below.

An online SMILES translator is available from the National Cancer Institute at For a brand new chemical substance, you usually need to draw its chemical structure using commercial software. The software will then give you the SMILES code.

In this case, we will enter the SMILES for the following substance and then click "insert".

  • Chemical name:  Ethanol, 2-((2-nitrophenyl)amino)-
  • CAS no.: 4926-55-0
  • Smiles: O=[N+]([O-])c1c(NCCO)cccc1

Toxtree SMILES

Step 4: Estimate Cramer Class

Click "Estimate" button on the right and you will see the estimated Cramer class marked in red. You can also see explanation s in result window. In this case, the compound is assigned to Cramer Class III due to NO2 functional group.

Toxtree Result

Step 5: Save File for Later Use

Click "File" -> "Save".

More Info

Having Questions?

We do not provide consultancy services. If you have questions or need any help, please contact our sponsor. You may also find an expert in CSP business directory below. If you are a consultant, you may get yourself listed in CSP business directory (free) or sponsor this page to leave your contact info on this page..

 Tags: Topics - CRAToxicology and Health Risk Assessment