A webserver for target prediction of bioactive small molecules

SwissTargetPrediction is a webserver for target prediction of bioactive small molecules in human and other vertebrates in order to understand the molecular mechanisms underlying a given phenotype or bioactivity, to rationalize possible side-effects or to predict off-targets of known molecules. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280'000 compounds active on more than 2000 targets of 5 different organisms.

Key features

  • 5 available organisms (Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Equus caballus)
  • Rapid prediction from a SMILES
  • For each query molecule, identification of the most similar molecules among a set of more than 300'000 known ligands from the ChEMBL database (version 16), which is the largest publicly available database of interactions between small molecules and proteins
  • Targets ranked according to a score that combines both 2D and 3D similarity values with the ligands most similar to the query molecule
  • Combination of different similarity measures for better accuracy and exploration of larger regions.


  • SwissTargetPrediction: a webserver for target prediction of bioactive small molecules, Nucl. Acids Res. (2014) (PDF)
  • Shaping the interaction landscape of bioactive molecules, Bioinformatics (2013) 29:3073-3079 (PDF)


SwissTargetPrediction is developed and copyrighted by SIB Swiss Institute of Bioinformatics and its exclusive commercial representative GeneBio.
Access is free for non-commercial use. Access by commercial entities is subject to the licensing conditions outlined in the GeneBio License Agreement (PDF).

Please contact us for further details.

SwissTargetPrediction website