Structural Similarity Search

Search is performed against the PubChem Compound Database or the ChEMBL 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.
  • EI algorithm: Searches the ChEMBL Compound database using the EI Search algorithm (Cao et. al. 2010) with an atom pair (AP) similarity measure.

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: