Search is performed against the PubChem Compound Database or the ChEMBL database, using one of two algorithm and database options:
PubChem 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.
ChEMBL Fingerprint algorithm: Searches the ChEMBL database.
EI algorithm: Searches the ChEMBL Compound database using the EI Search algorithm (Cao et. al. 2010) with an atom pair (AP) similarity measure.