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.