This page helps you try ChemAxon’s hERG training and prediction locally, on your machine.
Download the hERG trial ZIP package bundled with Java runtime for your OS from the link below:
After unzipping you will find two executable files in it that you can run in a command line environment, the
herg and 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.zippackage. Otherwise choose from the other ZIP packages with embedded Java for your OS.
To get started using hERG, run the
herg script in your command line interface:
This prints the help manual of the script and provides information on the available commands.
The following examples show how to use the
herg script for training and prediction.
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.
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.
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 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 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.
NOTE: If you would like to know more about Playground, please take a look at its documentation page.
The following steps will help you with the settings of your OS in case you get security warnings while trying to run the scripts.
When you double-click on the
playground script you can get the Java warning below.
Press Cancel, then go to the System Preferences » Security & Privacy tab and press Allow Anyway. This will allow Java to run.
Finally click Open. This will start Playground in your browser.
When you double-click on the
playground script you can get the system warning below. Click More info to proceed.
Click Run anyway to remove the OS protection.
If a firewall warning message appears, click the Cancel button. This still allows Playground to run locally.
This will start Playground in your browser.
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.