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Fig. 9 | Journal of Cheminformatics

Fig. 9

From: A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19

Fig. 9

Automated substructure searches in KNIME: The loop iterates through the input substructure queries (in SMARTS) to find hits in DrugBank (input data set includes molecules in SDF format, DrugBank IDs, and associated content). The structures from DrugBank are standardized (‘Standardization of structures’ metanode), and then subjected to the ‘RDKit Substructure Filter’ node to perform substructure searches. The SMARTS query is forwarded to the input as a variable. Detected substructures are highlighted by the ‘RDKit Molecule Highlighting’ node. The output table contains identified hits (molecule names, associated targets, SMARTS keys, chemical structures), and highlighted substructures in SVG format

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