Molecular Fingerprint Recombination: Generating Hybrid Fingerprints for Similarity Searching from Different Fingerprint Types

Abstract Molecular fingerprints have a long history in computational medicinal chemistry and continue to be popular tools for similarity searching. Over the years, a variety of fingerprint types have been introduced. We report an approach to identify preferred bit subsets in fingerprints of different design and “recombine” these bit segments into “hybrid fingerprints”. These compound class‐directed fingerprint representations are found to increase the similarity search performance of their parental fingerprints, which can be rationalized by the often complementary nature of distinct fingerprint features.