Created: 2013-08-13 07:40:04      Last updated: 2015-12-01 00:45:26

*** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries ***

The old Indigo library (1.1.13) could not take advantage of the parallelizing nodes in KNIME the way the RDKit library could. One way to speed up the PAINS workflow when using the Indigo library was to use a recursive loop that constantly shrank the list of structures being presented to the next PAINS query as structures were knocked out of the main list.

Using the WEHI-10k reference set (embedded in the workflow), I get ~10% time reduction. Not as good as parallelizing the process, but welcome nonetheless.

At the end of the process, the list of failures indicates only the first PAINS query that was matched, rather than multiple PAINS queries that were matched to that structure.

Otherwise, exactly the same number of hits (and structures) are obtained.

See 'Attributions' over on the right for other versions of this workflow.

If you like this workflow, please reference our paper doi:10.1002/minf.201100076.

The Indigo nodes require installation of the 'community nodes' in KNIME. See and

Based on simple sub-structure workflow by James Davidson
and recursive-loop filter workflow by Iris

Modified to use SD/SMILES file as input, or manual SMILES entry, or database search.


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