RDKit-pains

Created: 2011-02-07 02:05:36      Last updated: 2015-11-19 04:55:51

 If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflow Indigo-pains.

Implementation of the PAINS filters[1] using the RDKit (1.0.0.0000763) nodes in KNIME (2.3.1). 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 RDKit nodes require installation of the 'community nodes' in KNIME. See http://tech.knime.org/community-installation

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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  • Tuesday 04 October 2011 02:16:21 (UTC)

    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

  • Tuesday 01 September 2015 04:36:03 (UTC)

    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.

  • Thursday 19 November 2015 04:57:48 (UTC)

    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.




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