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Table 2 Evaluation and comparison of the performances of PEPOP

From: PEPOP: Computational design of immunogenic peptides

Ab – Ag complex1 PDB Epitope (number of amino acids) PEPOP CEP DiscoTope
    Number of clusters containing epitopic residues/total number of clusters Number of predicted residues of the epitope Sp Se PPV Sp Se PPV Sp Se PPV
D1.3 – hen egg lysozyme [54] 1SFG_A 10 1/4 10 0.77 1.00 0.27 0.76 1.00 0.26 0.80 0.40 0.14
D44.1 – hen egg lysozyme [56] 1T6V_M 11 1/5 11 0.81 1.00 0.33 0.78 0.91 0.28 0.86 0.55 0.27
HyHEL-5 – hen egg lysozyme [57] 1VDP_B 14 1/5 13 0.83 0.93 0.41 0.88 0.00 0.00 0.78 0.00 0.00
Jel42 – HPr [60] 1POH 16 2/8 13 0.93 0.81 0.72 0.90 0.75 0.63 0.97 0.06 0.33
D11.15 – hen egg lysozyme [55] 1HEL 10 2/5 8 0.95 0.80 0.57 0.90 0.10 0.08 0.82 0.30 0.13
5G9 – tissue factor [61] 1WV7_T 18 1/3 14 0.75 0.78 0.25 0.84 0.28 0.15 0.84 0.17 0.10
BH151 – hemagglutinin [62] 5HMG_C 19 3/7 12 0.83 0.63 0.19 0.97 0.32 0.40 0.75 0.11 0.03
Bo2C11 – FVIII C2 domain [63] 1D7P_M 15 3/5 8 0.92 0.53 0.42 0.94 0.47 0.44 0.83 0.53 0.25
NC41 – neuraminidase [64] 1NMC_N 22 3/4 11 0.90 0.50 0.23 0.99 0.59 0.81 0.85 0.64 0.20
F9.13.7 – guinea fowl lysozyme [65] 1HHL 10 3/5 5 0.98 0.50 0.71 0.92 0.50 0.33 0.83 0.40 0.17
HyHEL-10 – hen egg lysozyme [58] 1UC0_A 16 3/5 8 0.99 0.50 0.89 0.96 0.56 0.64 0.87 0.44 0.32
HyHEL-63 – hen egg lysozyme [59] 1VFB_C 23 3/4 9 0.82 0.39 0.32 0.73 0.30 0.19 0.87 0.39 0.39
N10 – staphylococcal nuclease [66] 1EYO_A 18 3/6 6 0.87 0.33 0.29 0.88 0.06 0.07 0.66 0.33 0.13
Average      0.87 0.67 0.43 0.88 0.45 0.33 0.83 0.33 0.19
Median      0.87 0.63 0.33 0.90 0.47 0.28 0.83 0.39 0.17
  1. 1 The corresponding reference is given in parentheses
  2. nd: not determined (no results returned from the server)
  3. Sp: specificity; Se: sensibility; PPV: positive predictive value (see Materials and methods)