A software to calculate pharmacodynamics, pharmacokinetics and toxicological properties of compounds.



The latest version of Java JRE (version 6) is recommended.


Download it from here. Unzip the files to any directory. Launch the software using "java -XX:MaxPermSize=256m -Xms1024m -jar PaDEL-DDPredictor.jar" without the double quotes. Alternatively, if you are in Windows, you can run the PaDEL-DDPredictor.bat file.

In the Settings tab
- Select a single structural file or a directory containing the molecules' structural files. Most common file formats (e.g. MDL mol, SMILES) are supported but the recommended file format is MDL mol.
- Select a file to save the predicted properties to. The properties will be saved in comma separated value (CSV) file format. The first row is the header row. Subsequent rows will contain the predicted properties for one compound per row. The first column is the compound's name, which is either obtained from the structural file or autogenerated (will be prefixed with AUTOGEN_ followed by the file name). Subsequent columns are the properties for the compounds.

In the Models tab
- Click on "Check for new models" button to check for new models. Check the required models and click on the "Install selected models" button to install them. - Check the required models and click on "Start" button to start the properties prediction.


This software is free for all (e.g. personal, academic, non-profit, non-commercial, government, commercial, etc) to use.


Please cite using: He YY, Liew CY, Sharma N, Woo SK, Chau YT and Yap CW (2013). PaDEL-DDPredictor: Open-source software for PD-PK-T prediction. Journal of Computational Chemistry. 34 (7): 604-610

Source code

Download the source code here. The source code is released as public domain. However, any part of the code that uses other libraries will still be restricted by the respective licenses.


The software is powered by JIDE. We acknowledge the provision of free single developer license by JIDE for this software.


  1. Version 2.1 [12 May 2015]: Updated software to check for updates.
  2. Version 2.0 [21 Jun 2012]: Updated GUI to use JIDE components. Enable software to be auto-updatable. Enable models to be downloaded and installed from within software.
  3. Version 1.0 [18 May 2011]: First release.

Last modified on 21 February, 2013 by Yap Chun Wei