We have made available a KNIME workflow on the MyExperiment.org site implementing the WEHI pan-assay interference structure (PAINS) filters using the Indigo sub-structure nodes.
The workflow contains the PAINS filters in SMARTS format, and a reference set of 10k SMILES strings from WEHI, which is used as input if you provide no other input. These can be used to compare results between other chemistry packages, or other versions of the PAINS filters.
We were hoping that our soon to appear paper describing this workflow would be released on the journal's web site by now (it was accepted a while ago), but in anticipation of the KNIME workshop later in the week, we're drawing the community's attention to the workflow.
The paper compares the original Sybyl/SLN system to RDKit/SMARTS and Indigo/SMARTS using KNIME.
It also re-emphasizes the need to pre-process your structures as described in the original PAINS publication before using the filters. The built-in reference set has been pre-processed according to that paper.
(the other) Simon