RDKit-pains
Download WorkflowIf you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains-parallel, and Indigo-pains.
*** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries ***
Implementation of the PAINS filters[1] using the RDKit (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This 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 the input if no other file is chosen.
The updated PAINS filters now remove 753 structures, which includes 2 false positives, from the reference set. The original SLN filters remove 861.
For a faster workflow that uses all the cores in a multi-core processor, see RDKit-pains-parallel http://www.myexperiment.org/workflows/2485
This workflow continues to use only those nodes that were available at the time in 2010. For a more compact workflow by Evert Homan using more recently available RDKit nodes, see http://www.myexperiment.org/workflows/4748.html
The RDKit nodes require installation of the 'community nodes' in KNIME. See https://tech.knime.org/community
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. See discussion http://sourceforge.net/p/rdkit/mailman/message/34405703/ and the file in the repository https://github.com/rdkit/rdkit/tree/master/Data/Pains
3. 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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RDKit 2.0.0.1088 now matches 636 structures, up from 329 reported in our paper, but matches 2 additional structures not matched by the SLN filters.
See discussion on RDKit list: http://goo.gl/NVIgy
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.
RDKit nodes are now available in KNIME 3, so version 4 is now based on KNIME 3.0.1 and the updated PAINS filters from the RDKit repository.