These results bring to light the difficulty to foresee beforehand which peptide lengths or scaffolds will lead to the optimal peptide sequence. The same way, starting from one peptide length or scaffold does not guarantee that knowledge can be easily transferred to others if a correlation exists between sequence binding profiles and peptide lengths or scaffolds. As the method do not seem to be compromised by a lesser representation of each peptide length when using the MAP4 fingerprint method, one could leverage on information from multiple protein-peptide complex structures, and predictions based on them, and start with a diverse set of peptide sequences as the initial batch. This strategy, supported by our results, emphasizes the importance of diversity in the initial batch, especially when precise knowledge of the optimal peptide length is absent.