Created: 2011-06-07 00:39:29      Last updated: 2015-12-01 00:45:02

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

Implementation of the PAINS filters[1] using the Indigo ( nodes in KNIME (2.3.4). Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by the Guha group[2]. Also distributed with a 10k reference structure set from WEHI[1] which is used by default as input if no other file is chosen.

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

Based on simple sub-structure workflow by James Davidson
Modified to use SD/SMILES file as input, or manual SMILES entry, or database search.

1. J. B. Baell and G. A. Holloway, Journal of Medicinal Chemistry, 2010, 53, 2719-2749,

2. Rajarshi Guha. "PAINS Substructure Filters as SMARTS. 2010-11-14." Accessed: 2010-11-14. (Archived by
WebCite® at

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  • Friday 22 July 2011 14:25:16 (UTC)

    If you are having difficulty running large data sets, edit your knime.ini file and change the -Xmx value to increase the memory available to KNIME. A 300k SMILES set can be processed easily with -Xmx1500m.

  • Tuesday 01 September 2015 04:36:43 (UTC)

    The updated PAINS filters from the RDKit developer are resulting in improved results:

    Just waiting on the nodes to be updated in KNIME before updating the workflows here, but you can grab the filters from the above link if you can't wait.

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