I am using Pepspec to optimize a 10mers peptide sequence to better binding to a membrane protein. In the design, I kept the first residue constant, while mutating the rest by all 20 amino acids. The flags file is the following:
The run generated 990668 non-redundant sequences and saved 10000 pdbs. Then I used WebLogo to evaluate the quality of the sampling (see attached picture). As can be seen, there is an over-enrichment of Ser and Gly along the sequence, which looks weird to me. Is this an artifact of the sampling? How can I improve the sampling?
Thanks in advance,