PAINS Filter: What It Is and Why Your Docking Hits Fail It

By BioDockify Computational Research Team · September 3, 2026 · Concepts

PAINS filters explained: the reactive substructures that fake docking hits, the most common offenders, how to run the filter, and when a flagged hit is salvageable.

Read the complete article with tables, code and references on BioDockify.

Key References

• Baell JB, Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem. 2010;53(7):2719-2740. doi:10.1021/jm901137j
• Baell J, Walters MA. Chemical con artists foil drug discovery. Nature. 2014;513(7519):481-483. doi:10.1038/513481a
• RDKit documentation: PAINS and other alert filters in the FilterCatalog module, rdkit.org.

Scope & Limitations

A PAINS alert is a probability statement, not a verdict; the filter flags frequent-hitter substructures and does not measure the actual behavior of your specific compound in your specific assay