Evert Homan's Workflows

RDKit Aggregator Advisor (1)

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A Knime (2.12.1) workflow that uses RDKit nodes for assessing the risk of a compound to form aggregates under biochemical assay conditions, inspired by the Aggregation Advisor paper of Irwin et al. While the Aggregator Advisor web tool allows for aggregation risk assessment of individual compounds, this Knime workflow can be used to quickly run through large compound collections.Query structures are loaded as an SD file (here a set of 1090 approved drugs), and are then compared for Tanimoto s...

Created: 2015-10-18 | Last updated: 2015-10-18

Credits: Evert Homan

RDKit PAINS 4 (1)

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Improved Knime (2.12.1) workflow for detection of Pan-Assay Interference Compounds (PAINS) using RDKit nodes. PAINS SMARTS curated by Greg Landrum are used for the substructure searches. These yield 753 hits among the WEHI set of 10,000 compounds. A Total Hits count column is added by the RDKit Substructure Counter node, so no additional aggregation is needed. Structures devoid of PAINS are separated out for further progression, while the PAINS hits can be visually inspected using the RDKit I...

Created: 2015-10-18 | Last updated: 2015-10-18

Credits: Evert Homan