Figure 2.

Search algorithm flow strategy. An initial peptide sequence is chosen (in this instance peptide P6). Random numbers were generated to determine whether to mutate one amino acid or not (“No” or “Yes”). If yes, then one amino acid from the sequence was randomly changed to an amino acid from the same residue category (Table 1). If no, then two amino acids from the sequence were randomly exchanged regardless of the residue category. The SCMF algorithm was then used to determine the lowest-energy rotamer combination. The MC algorithm was used to accept or reject the newly generated peptide sequence based on the calculation of binding free energy (ΔG¹_binding).