** Example 1: **Epitopia prediction for vascular endothelial growth factor (VEGF) protein structure (PDB ID 1bj1, chain W)

The immunogenic potential of the surface of VEGF as computed by Epitopia is presented in Figure 1. Figure 1A displayes a sample of the actual immunogenicity and probability scores computed by Epitopia for each surface residue of VEGF. Figure 1B presents a snapshot of the graphical output given by the FirstGlance in Jmol visualization tool. Figure 1C presents the graphical output as displayed using Rasmol, where chains L and H of the anti-VEGF murine monoclonal antibody are displayed in backbone mode. It is evident that the most immunogenic residues predicted by epitopia significantly overlap the true epitope of the anti-VEGF murine monoclonal antibody.

Figure 1 |

** Example 2: **Epitopia prediction for Plasmodium falciparum Merozoite surface antigen 2 (MSA-2) sequence (Swiss-Prot: P19599)

The immunogenic potential of the MSA-2 protein as computed by Epitopia is presented in Figure 2. Figure 2A presents a sample of the actual immunogenicity and probability scores computed for each residue in the sequence. Figure 2B presents the graphical output of the prediction. Figure 2C presents a sample of the clusters of immunogenic regions.

Figure 2 |