We used the Jaccard-Tanimoto similarity to assess pairwise similarities between compounds for all fingerprints. For categorical fingerprints (MAP4 and MHFP), we used a modified version of the Jaccard-Tanimoto similarity which considers two bits as a match if they contain exactly the same integer, as introduced in a previous study. To ensure comparability, count-based fingerprints were converted into binary bits, by only encoding whether a fragment is present or absent, and then pairwise similarities were measured as for the other encodings. This ensures that any variation in pairwise similarities between two fingerprint types is exclusively related to differences in how the vectors are computed, and not due to using different metrics.