Structural Similarity Search

Search is performed against the PubChem Compound Database using one of two algorithm and database options:

  • Fingerprint algorithm: Searches a "cleaned up" version of the PubChem Compound database (excluding some very similar compounds and some salts) by connecting to the PubChem web interface using the PubChem Fingerprint similarity measure. As this connects directly to PubChem, it will include new compounds sooner than the EI search.
  • EI algorithm: Searches the full PubChem Compound database (including very similar compounds and salts) using the EI Search algorithm (Cao et. al. 2010) with an atom pair (AP) similarity measure. NOTE: EI Search is currently undergoing updates and may be missing some results.

Algorithm and database:

The center dot is a carbon atom. To add bonds, choose a bond type and click the central atom. To replace atoms, choose an element and click the atom you would like to replace.


Algorithm and database:

Please copy and paste your single-molecule SDF below. If multiple compounds are supplied, only the first one will be used.


Algorithm and database:

Please upload a single-molecule SDF below. If multiple compounds are found in the SDF, only the first one will be used.

Algorithm and database: