Public server:
Summary:For processing, analysing and visualising chemical data, and performing molecular simulations.


  • A set of almost one hundred tools integrated into the Galaxy-workflow-management system to enable researchers easy-to-use, reproducible, and transparent access to cheminformatics libraries and drug discovery tools. It includes standard applications for similarity and substructure searches, clustering of compounds, prediction of properties and descriptors, filtering, and many other tools that range from drug-likeness classification to fragmentation and fragment-merging. By combinating the various tools many more powerful applications can be designed.
  • The public server is hosted by the team.
  • ChemicalToolBox can be installed locally from the toolshed by means of a metapackage containing all other dependencies, e.g. chemfp, openbabel, osra, confab, rdkit. See the ChemicalToolBox ToolShed repository.
  • We set up an example workflow to for the preparation of a large compound library by merging of chemical databases. This workflow is part of case study demonstrating the capability of the chemicaltoolbox. For further information please have a look at the chemicaltoolbox .

User Support


  • Server: Storage and computational quotas.
  • Docker: None.