On the other hand, molecular fingerprints are not dependent on the size of the peptide sequences, allowing comparison between peptides of different lengths, or also peptides containing macrocycles, non-natural amino acids or other chemical modifications such as phosphorylation. In this work, we used the following molecular fingerprints: MinHashed Atom Pair (MAP) fingerprint , MinHash fingerprint (MHFP) and the commonly used morgan fingerprint for small molecules. As part of the extended-connectivity fingerprint (ECFP) family, a parameter r (radius) or d (diameter) can be specified for each of these fingerprints to take into account the circular environment of each atom (circular substructure), with a larger r or d associated to a more detailed perception of the local environment. To find the optimal parameters for each fingerprint method, multiple diameters (2 or 4) and fingerprint sizes (2048 and 4096) were tested.