RDKit-pains-parallel

 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 (2.0.0.1088) nodes in KNIME (2.5.0).

Parallel processing nodes added to take advantage of mutil-core processors.

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)