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, and check the related workflows Indigo-pains-recursive, and RDKit-pains.

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

Implementation of the PAINS filters[1] using the Indigo (1.1.1300.201511201230) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. his workflow contains the SMARTS form of the filters published by Greg Landrum as part of the RDKit library[2], which are based on the original conversion by the Guha group[3]. 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 updated PAINS filters now remove 825 structures from the reference set. The original SLN filters remove 861.

For a faster workflow that uses a recursive loop, see Indigo-pains-recursive

This workflow continues to use only those nodes that were available at the time in 2010.

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. See discussion and the file in the repository

3. 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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