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KNIME-CDK: Workflow-driven cheminformatics

Stephan Beisken1*, Thorsten Meinl2, Bernd Wiswedel3, Luis F de Figueiredo1, Michael Berthold2 and Christoph Steinbeck1

Author Affiliations

1 European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

2 Nycomed Chair for Bioinformatics and Information Mining, University of Konstanz, Konstanz, Germany

3 AG, Technoparkstr. 1, 8005 Zürich, Switzerland

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BMC Bioinformatics 2013, 14:257  doi:10.1186/1471-2105-14-257

Published: 22 August 2013



Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process.


KNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest.


KNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment.

Cheminformatics; Workflows; Data integration; Software library