Abstract
The ever growing size of chemical databases calls for the development of novel methods for representing and comparing molecules. One such method called LINGO is based on fragmenting the SMILES string representation of molecules. Comparison of molecules can then be performed by calculating the Tanimoto coefficient, which is called LINGOsim when used on LINGO multisets. This paper introduces a verbose representation for storing LINGO multisets, which makes it possible to transform them into sparse fingerprints such that fingerprint data structures and algorithms can be used to accelerate queries. The previous best method for rapidly calculating the LINGOsim similarity matrix required specialized hardware to yield a significant speedup over existing methods. By representing LINGO multisets in the verbose representation and using inverted indices, it is possible to calculate LINGOsim similarity matrices roughly 2.6 times faster than existing methods without relying on specialized hardware.
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