ChemAxon’s hERG trial guide

This page helps you try ChemAxon’s hERG training and prediction locally, on your machine.

Table of Contents

Downloading the hERG trial package

Download the hERG trial ZIP package bundled with Java runtime for your OS from the link below:

hERG trial package

After unzipping you will find two executable files in it that you can run in a command line environment, the herg and the playground scripts.

The herg script allows you to run ChemAxon’s hERG training and prediction, while the playground script starts ChemAxon’s Playground web application in your browser.

NOTE: If you have Java version at least 1.8 installed on your computer we recommend that you download the hERG-predictor-21.10.zip package. Otherwise choose from the other ZIP packages with embedded Java for your OS.

hERG training and prediction

To get started using hERG, run the herg script in your command line interface:

./herg

This prints the help manual of the script and provides information on the available commands.

Examples

The following examples show how to use the herg script for training and prediction.

Example 1

Predicting hERG using the default ChemAxon hERG model, with both input (molecules.sdf) and output (result.sdf) given as SD files:

./herg predict -S -i molecules.sdf -o result.sdf

INFO: The default ChemAxon hERG model was built from almost 2100 compounds with hERG data coming from ChEMBL and other sources.

Example 2

Predicting hERG using the extended ChemAxon hERG model (also available in the ZIP package as hERG-extended-model.ser), with an SD file (molecules.sdf) given as input and returning the results to the standard output (in TSV format):

./herg predict -m hERG-extended-model.ser -i molecules.sdf

INFO: The default ChemAxon hERG model has been extended with hERG active compounds with pAct values > 6.6 from the hERG Central Database.

Example 3

Creating a hERG training model from a training set given as an SD file (training.sdf) with hERG pAct values stored in a hERG_EXP SD file tag and storing the result in a model file (hERG_v1.ser):

./herg train --training-set training.sdf --sdf-tag “hERG_EXP” -o hERG_v1.ser

Then using this created hERG model to predict hERG activity for molecules given as an SD file (molecules.sdf) and returning the results to the standard output (in TSV format):

./herg predict -m hERG_v1.ser -i molecules.sdf

NOTE: If you would like to know more about ChemAxon’s hERG Predictor, please take a look at its documentation page.

Playground

Playground is an interactive web application for various property calculations, including hERG.

To run Playground either double-click on the playground script in the unzipped package or run it from command line. Both start the web application in your browser.

To run the hERG prediction in Playground select hERG in the Explore Calculations menu. The default calculation is pKa.

readme_pg_herg

NOTE: If you would like to know more about Playground, please take a look at its documentation page.

Troubleshooting on your OS

The following steps will help you with the settings of your OS in case you get security warnings while trying to run the scripts.

MacOS

When you double-click on the playground script you can get the Java warning below.

readme_macos_java_warning

Press Cancel, then go to the System Preferences » Security & Privacy tab and press Allow Anyway. This will allow Java to run.

readme_macos_java_allow

Finally click Open. This will start Playground in your browser.

readme_macos_java_open

Windows

When you double-click on the playground script you can get the system warning below. Click More info to proceed.

readme_win_more_info

Click Run anyway to remove the OS protection.

readme_win_run

If a firewall warning message appears, click the Cancel button. This still allows Playground to run locally.

readme_win_allow

This will start Playground in your browser.

Licensing

The ZIP package contains an evaluation license that allows you to use the scripts until the 31st May 2021. After expiry please contact [email protected] to extend your license.