Modeling the adaptive immune system: predictions and simulations

Lundegaard, Claus; Lund, Ole; Kesmir, Can; Brunak, Søren; Nielsen, Morten

Different ways of measuring the accuracy of B-cell epitope predictions have been suggested (Hopp, 1994; van Regenmortel and Pellequer, 1994) . Pellequer suggested using the specificity as a measure of accuracy, while Hopp suggested using the PPV, but, as described earlier, neither measure will alone give a good description of the performance. In accordance to this the recent workshop concluded that the AUC measure is to be preferred (Greenbaum et al., 2007) . Another issue is whether to make the statistics on a per-residue or on a per-epitope basis. However, as the latter have the additional complications of defining how much of an epitope that must be included in a prediction to be considered correct, and how much extra included residues is allowed, the per residue measure is to be preferred.