Table 1. Filters for PAINS and promiscuous compounds.
| Filter | URL | Description | Input Format |
|---|---|---|---|
| FAFdrugs4 | http://fafdrugs4.mti.univ-paris-diderot.fr | Predicts ADME parameters’ physicochemical characteristics, PAINS filtering using predefined or custom filtering parameters. Optional use of Eli Lilly and original PAINS compendium [6]. | SDF |
| ZINC | http://zinc15.docking.org/patterns/home | PAINS and aggregate filter. PAINS definitions based on the original compendium [6]. | SMILES, ZINC ID, InChl, SMARTS |
| SwissADME | swissadme.ch | Calculates physicochemical characteristics, drug-like properties, pharmacokinetic properties, and PAINS filtering and predicts ADME parameters. PAINS definition based on the original compendium [6]. | SMILES |
| PAINS-Remover | http://www.cbligand.org/PAINS/ | PAINS filter; definitions based on the original compendium [6]. | SMILES |
| Knime | https://www.knime.com/forum/indigo/pains-filter-workflow | Online workflow for PAINS filtering; definitions based on the original compendium [6]. | SMARTS |
| Badapple | http://pasilla.health.unm.edu/tomcat/badapple/badapple | Second-generation filter algorithm, moving beyond substructure searches to identify potential promiscuous compounds from database of known scaffolds. Uses the Molecular Libraries Small Molecule Repository (MLSMR) database of compounds and PubChem HTS assays. Total structure library is approximately 390,692 compounds [18]. | SMILES |
| Aggregator Advisor | advisor.bkslab.org | Identifies molecules that may or have been shown to aggregate in biochemical assays. Based on physical properties and chemical similarity to known aggregators. | SMILES |
Note the potential for translation issues from the original SLN PAINS filter language into SMARTS [10]. Abbreviations: ADME, absorption, distribution, metabolism, and excretion; HTS, high-throughput screening; InChI, international chemical identifier; MLSMR, Molecular Libraries Small Molecule Repository; PAINS, pan-assay interference compounds; SDF, structure-data file; SLN, SYBYL line notation; SMARTS, SMILES arbitrary target specification; SMILES, simplified molecular-input line-entry system.