Indigo-pains
Download WorkflowIf you like this workflow, please reference our paper doi:10.1002/minf.201100076.
Implementation of the PAINS filters[1] using the Indigo (1.0.0.0000951) 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 http://tech.knime.org/community-installation and http://ggasoftware.com/opensource/indigo/knime
Based on simple sub-structure workflow by James Davidson
http://tech.knime.org/forum/rdkit/substructure-search-with-rdkit
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, http://dx.doi.org/10.1021/jm901137j
2. Rajarshi Guha. "PAINS Substructure Filters as SMARTS. 2010-11-14."
http://blog.rguha.net/?p=850. Accessed: 2010-11-14. (Archived by
WebCite® at http://www.webcitation.org/5uF4wHEpB)
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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.
The updated PAINS filters from the RDKit developer are resulting in improved results:
http://rdkit.blogspot.com/2015/08/curating-pains-filters.html
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.