Baell and Holloway published a set of substructure filters for removal of what they termed “Pan Assay Interference Compounds (PAINS)” from screening collections [J. Med. Chem. 2010 53(7) pp. 2719-2740]. These define functional groups that are known to cause problems due to reactivity, poor development potential or known toxicity and have been widely adopted. You can download these filters as SMARTS for use within StarDrop here.
The original PAINS filters were defined in Sybyl Line Notation (SLN) and were converted to SMARTS by Rajarshi Guha using the Cactvs library. Rajarshi Guha notes that the conversion was not perfect.
The SMARTS files created by Rajarshi Guha have been converted into a form that can be easily imported into StarDrop for use in the data set filtering tool (Data Set->Filter menu option) or in the Nova module. These can be downloaded from the following links:
PAINS_S6 : Table S6 from the supplementary information of Baell and Holloway.
PAINS_S7 : Table S7 from the supplementary information of Baell and Holloway.
PAINS_S8 : Table S8 from the supplementary information of Baell and Holloway.
As an alternative, you can also download a model for StarDrop that counts the number of PAINS matches for each compound. This has advantages over filters in that the PAINS matches can be visualised in StarDrop’s Glowing Molecule and the match count can be included in a scoring profile to give it appropriate weight against other considerations in the prioritisation of your compounds.
The short video below demonstrates how to import the PAINS filters SMARTS files into StarDrop: