This page provides you with an overview of all our open source software tools, including download links and manuals. A list of references that cite our tools can be found in the about section. Follow us on Google groups to receive news about updates and tools, or if you want to raise questions or propose suggestions for further improvements.

Command-line tools

img_filterit Filter-it™ is a command-line program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre-programmed molecular properties that can be used for filtering.

version 1.0.2>   manual | download

img_stripit Strip-it™ is a tool to extract molecular scaffolds according predefined rules based on definitions as described by Murcko (J. Med. Chem. 1996, 39, 2887), Pollock (J. Chem. Inf. Model. 2008, 48, 1304) and Schuffenhauer (J. Chem. Inf. Model. 2007, 47, 47).

version 1.0.2>   manual | download

img_alignit Align-it™ is a pharmacophore-based tool to align molecules by representing pharmacophoric features as Gaussian 3D volumes. The smooth nature of these continuous functions has a beneficent effect on the optimisation problem introduced during alignment.

version 1.0.4>   manual | download

img_shapeit Shape-it™ is a shape-based alignment tool that represents molecules as a set of atomic Gaussians. The software is based on the alignment method described by Grant and Pickup (J. Phys. Chem. 1995, 99, 3503).

version 1.0.1>   manual | download

RDKit packages and libraries

img_biscuit Biscu-it™ is a collection of useful Python functions and C++ libraries that are build on top of the RDKit open source chemoinformatics toolkit of Greg Landrum. Requires a working installation of RDKit and Python.

>   more information

R packages

img_somit Som-it™ has been developed with the purpose to analyse R-generated SOM maps derived from extreme large datasets. The current package comprises a single tool for the projection and analysis of self-organising maps that were generated using R.

version 1.0.1>   manual | download

Free software foundation


Current projects

  • Optimisation of novel PPI's
  • Design of anti-viral compounds
  • Novel fragment-based descriptors

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