Predicting the likely conformations of amino acid residues—such as h, e, and coils or loops (c)—provides valuable structural insights for peptide designers. Specifically, residues predicted to form coils or loops often serve as a strong foundation for selecting peptides in the design of diagnostics and vaccines. This utility holds true regardless of the prediction's exact accuracy or other overlapping factors like water-liking character, exposure, or intrinsic immunogenicity.

Santa Clara University

Google

The probability of peptides being able to help with therapeutics and vaccines are becoming more relevant in clinical genomics that involved patient DNA sequences. The homologies that match viral protein sequences and uses of automated probabilistic reasoning are becoming more relevant.
The Q-UEL system has helped develop a preliminary set of predictive 3D protein structures of the virus.

Theory about peptides as the base of potential therapeutic and vaccines

When designing synthetic peptides for diagnostics or vaccines, several sequence-level suggestions apply:
- Avoid extensive stretches of strongly nonpolar (hydrophobic) amino acids.
- Remember that some epitopes serve a dual B-cell and T-cell epitope role.
- Avoid N-terminal asparagine (N) or glutamine (Q), and C-terminal proline (P) or glycine (G).

Potential concerns to address include:
- Lack of biostability (susceptibility to proteolysis).
- Whether the peptide can raise antibodies.
- Implanting immune-system memory in the case of vaccines.
- Specificity, i.e., avoiding unwanted cross-reactions with other proteins whose epitopes are similar to the target protein of interest.

Suggestions and concerns for synthetic peptides

L peptide:
-B epitope synthesized with L amino acids that can attach to a carrier and raise antibodies as diagnostic of as a potential vaccine. 
-Concerns: L peptide is susceptible to proteolysis from human proteins. The B epitope antigenic determinants for antibody production are discontinuous section fo sequence and could deliver poor results

D peptide:
- synthesis from D amino acid to act as an antagonist to viral entry
- has a much longer half-life to work at binding to ACE2

Proposed design for synthetic peptides

- Has only be used in the veterinary environment but there is hope that it could be useful for humans
- Concern that the concentrations required for the synthetic peptide to work can cause issues with effects on blood pressure. Aerosol could be useful instead. 
- Using the combination of bioinformatics, human researchers, Q-UEL tools, that there will be rapid access to fighting against viruses and other pathogens

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