Secure molecular similarity calculations

A method for securely sharing molecular structure information, the method comprising:

• generating a permutation operator;
• applying the permutation operator to a fingerprint representation of the molecular structure stored on a computer, thereby creating a permuted fingerprint;
• and
• sharing the permuted fingerprint, but not the permutation operator, with a third party.

A method for securely sharing a database of molecular structures, the method comprising:

• generating a permutation operator;
• applying the permutation operator to a fingerprint representation of each of the molecular structures in the database;
• and
• sharing the permuted fingerprint representations, but not the permutation operator, with a third party.

A method of calculating the similarity between a target molecule and molecules in a database, the method comprising:

• generating a permutation operator;
• applying the permutation operator to a fingerprint representation of the target molecular structure and fingerprint representations of the molecules in the database;
• and
• calculating the similarity between the target molecule and the molecules in the database by computing an overlap of their respective permuted fingerprints.

A computing apparatus for transforming a molecular fingerprint, the apparatus comprising:

• a memory;
• and
• a processor;
• wherein the processor is configured to execute instructions stored in the memory, and wherein the instructions comprise instructions for:
• generating a permutation operator;
• applying the permutation operator to the fingerprint;
• and
• storing the permuted fingerprint.