What do the ElliPro scores mean?
ElliPro is based on the concept that residues protruding from a protein's globular surface can be considered epitope candidates. The globular surface is modeled as an ellipsoid encompassing a specified percentage of the protein atoms. ElliPro computes a score for each residue of the input sequence. The score is the Protrusion Index of the residue, which is defined as the percentage of the protein atoms enclosed in the ellipsoid at which the residue first become lying outside the ellipsoid. For example, all residues lying outside the 90% ellipsoid will have scores >= 0.9. The score for a predicted epitope equals the average of the scores of each residue comprising the epitope.
Further information can be found in the tutorial (http://tools.immuneepitope.org/tools/ElliPro/tutorial.jsp) and in the article by Ponomarenko et al (PMID: 19055730), which can be downloaded from BioMed Central or the IEDB website (http://tools.immuneepitope.org/main/pdfs/ElliPro.pdf).