A new set of KNIME nodes implementing the QPhAR algorithm

Dissemination of novel research methods, especially in the form of chemoinformatics software, depends heavily on their ease of applicability for non‐expert users with only a little or no programming skills and knowledge in computer science. Visual programming has become widely popular over the last...

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Bibliographic Details
Published in:Molecular informatics 2023-05, Vol.42 (5), p.e2200245-n/a
Main Authors: Kohlbacher, Stefan M., Ibis, Gökhan, Permann, Christian, Bryant, Sharon, Langer, Thierry, Seidel, Thomas
Format: Article
Language:English
Subjects:
Algorithms
Best practice
Biological activity
Data processing
KNIME
NeuroDeRisk
Nodes
pharmacophore modeling
pharmacophores
Pipelining (computers)
Programming
QPhAR
Research methods
Skills
Software
Workflow
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Summary:Dissemination of novel research methods, especially in the form of chemoinformatics software, depends heavily on their ease of applicability for non‐expert users with only a little or no programming skills and knowledge in computer science. Visual programming has become widely popular over the last few years, also enabling researchers without in‐depth programming skills to develop tailored data processing pipelines using elements from a repository of predefined standard procedures. In this work, we present the development of a set of nodes for the KNIME platform implementing the QPhAR algorithm. We show how the developed KNIME nodes can be included in a typical workflow for biological activity prediction. Furthermore, we present best‐practice guidelines that should be followed to obtain high‐quality QPhAR models. Finally, we show a typical workflow to train and optimise a QPhAR model in KNIME for a set of given input compounds, applying the discussed best practices.
ISSN:1868-1743
1868-1751
DOI:10.1002/minf.202200245