In total, 27 unique combinations were generated from the 10 selected protein-peptide complex structures. Since there is only one protein-peptide complex co-crystallized with an 8-mers peptide, predictions using this structure were common to all combinations. The outcome was compared to the homolog scanning strategy. The co-crystallized peptides were used as input for the homolog scanning strategy. To form the initial batch, 24 peptides per length were generated using the homolog scanning strategy (e.g. 24 peptides generated from the 8-mers peptide, 24 from the 9-mers, 24 from the 10-mers and 24 from the 11-mers), totaling 96 peptides. For the random search, five different batches of 96 peptides of random lengths from 8-to 11-mers, corresponding to the total number of DMT cycles, were randomly generated.