KNIME-CDK: Workflow-driven cheminformatics

BMC Bioinformatics

Christoph Steinbeck³  Michael Berthold¹  Luis F de Figueiredo³  Bernd Wiswedel²  Thorsten Meinl¹  Stephan Beisken³ 

[1]Nycomed Chair for Bioinformatics and Information Mining, University of Konstanz, Konstanz, Germany

[2]KNIME.com AG, Technoparkstr. 1, 8005 Zürich, Switzerland

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

关键词: Software library;    Data integration;    Workflows;    Cheminformatics;   

Others  :  1087779
DOI  :  10.1186/1471-2105-14-257

 received in 2013-01-15, accepted in 2013-08-21,  发布年份 2013

【 摘 要 】

Background

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.

Results

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.

Conclusions

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.

【 授权许可】

   
2013 Beisken et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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