# US 2014/0156679 A1 · Secure molecular similarity calculations > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2014/0156679 A1 - Document ID: US20140156679A1 - Status: Published application - Kind: A1 - Application number: 13/920,010 - Filed: 2013-06-17 - Published: 2014-06-05 - Earliest claimed: 2012-06-17 - Assignees: OpenEye Scientific Software, Inc. - Applicants: OpenEye Scientific Software, Inc. - Inventors: Robert W. Tolbert; Joseph J. Corkery; Anthony Nicholls; Kevin Schmidt; Brian Kelley - Web page: https://patentgrep.com/patent/US20140156679A1 ## CPC - G06F 16/284: {Relational databases} - G06F 16/258: {Data format conversion from or to a database} - G06F 21/62: Protecting access to data via a platform, e.g. using keys or access control rules - G06F 21/6227: {where protection concerns the structure of data, e.g. records, types, queries} - G16C 20/80: Data visualisation - H04L 65/403: Arrangements for multi-party communication, e.g. for conferences (data switching systems for conference H04L12/18; arrangements for connecting several subscribers to a common circuit, i.e. affording conference facilities H04M3/56; television conferencing systems H04N7/15) - G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N) - G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE - H04L: TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION (arrangements common to telegraphic and telephonic communication H04M) ## Abstract Methods of securing the calculation of pairwise molecular similarity coefficients between molecules, from similarity measures that are based on 3-dimensional or 2-dimensional molecular properties and/or physicochemical properties, condensed into a fingerprint or bit-string representation, in such a way that a third party cannot deduce information about the underlying molecular structures. The apparatus and process are particularly applicable to generating secured or anonymized databases of bit-strings, so that the anonymized databases can be stored remotely from a corporation's computer system, or shared securely and confidentially with another company. The mapping key that permits the anonymized bit strings to be converted back to their original form need not be disclosed outside of the corporation. The methods also permit two companies to exchange molecular structure data securely and in a manner that permits similarity calculations to be performed within as well as between the respective databases. ## Claims ### Claim 1 A method, performed on a computer, of transforming a fingerprint representation of a molecule, the method comprising: generating a permutation operator; applying the permutation operator to the fingerprint, wherein the fingerprint is stored in a computer memory, thereby generating a permuted fingerprint; and storing the permuted fingerprint in computer memory. ### Claim 2 (depends on 1) The method of claim 1, wherein the fingerprint is a bit-string. ### Claim 3 (depends on 2) The method of claim 2, wherein the bit-string comprises positions that correspond to one or more of: presence of a particular functional group or groups in the molecule; presence of one or more particular bond paths in the molecule; presence of one or more particular bond trees in the molecule; whether the molecule is active or inactive in a particular test according to screening data; and whether a docking score is above a threshold value in a virtual screen. ### Claim 4 (depends on 1) The method of claim 1, wherein the fingerprint comprises positions that correspond to one or more of: numerical physicochemical data for the molecule; electrostatic field data at a position in a grid representation of the molecule; and histogrammed data for a molecular property. ### Claim 5 (depends on 1) The method of claim 1, wherein the molecular fingerprint is stored in a database on a computer, and wherein the method is applied to at least one other molecular fingerprint in the database. ### Claim 6 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. ### Claim 7 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. ### Claim 8 (depends on 7) The method of claim 7, further comprising inserting one or more fictitious fingerprint representations at random positions in the database. ### Claim 9 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. ### Claim 10 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.