Abstract
BackgroundCheminformaticians 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.ResultsKNIME-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.ConclusionsKNIME-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.
Highlights
Cheminformaticians have to routinely process and analyse libraries of small molecules
The Konstanz Information Miner (KNIME) [7] is an open-source workflow platform that supports a wide range of functionality and has an active cheminformatics/bioinformatics community, e.g., with plug-ins for generation sequencing or image analysis [8,9,10]
We presented KNIME-Chemistry Development Kit (CDK), an open-source cheminformatics plug-in for the KNIME platform
Summary
Cheminformaticians have to routinely process and analyse libraries of small molecules. 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. The routine work of a cheminformatician involves the processing of libraries of small molecules. Standardising molecules, e.g., adding hydrogens or removing unconnected structures, calculation of molecular descriptors, and visualisation of chemical structures in two- or threedimensional space are just a few examples of recurrent tasks that are carried out upstream of cheminformatic pipelines. For a detailed description of the KNIME data analysis platform see [11]
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