A 20 residue acid sliding window that moved from the N to the C terminus of the E protein in 10 residue acid increments was evaluated by a structural stability (pseudoenergy) optimization protocol using the RAPDF. A Metropolis Monte Carlo search algorithm [38] was used to change each amino acid in the 20 residue window to one of the other 19 naturally occurring amino acids, and the stability of corresponding peptide in the context of the entire E protein structure was evaluated. This process was iterated 100,000 times using RAPDF as the target scoring function. The Metropolis criterion was used to select a particular change in the simulation: if a particular change resulted in a better RAPDF score (lower pseudoenergy), then it was retained. If a particular change resulted in a worse RAPDF score (higher pseudoenergy), then a random choice, based on the score difference between the previous change and the current one, was made to retain the corresponding change. This procedure enables not only enables design of peptides that will result in high structural and binding stability (i.e., the best RAPDF scores/ pseudoenergies), but also enables surmounting local minima encountered during the search. Computational optimization was performed on the four regions corresponding to the best RAPDF score, and therefore the highest binding potential, within the E protein as described above to generate variant peptides sequences.