Table 4.
Prediction of MHC class I specific peptide epitopes
| Start | Peptide | MHC-I binding scorea | Proteosomal Cleavage scoreb | Allele (Human Leukocyte Antigen [HLA] specific) |
Antigenic Scorec |
|---|---|---|---|---|---|
| 59 | YYYHASVTD | 1.3–17.0 | 0.82 | HLA-A*24:02,HLA-A*23:01,HLA-A*29:02,HLA-B*18:01,HLA-B*39:01, HLA-B*48:01,HLA-B*51:01,HLA-C*01:02,HLA-C*03:03,HLA-C*06:02, HLA-C*07:01,HLA-C*07:02,HLA-C*07:04,HLA-C*12:02,HLA-C*14:02, HLA-C*16:01,HLA-G*01:01,HLA-G*01:02,HLA-G*01:03,HLA-G*01:04, HLA-G*01:06 |
0.9572 |
| 95 | GFTDRGWGK | 4.4–15.5 | 0.85 | HLA-A*03:01,HLA-A*11:01,HLA-A*29:02,HLA-A*30:01,HLA-A*33:03, HLA-A*31:01,HLA-A*68:01,HLA-A*74:01,HLA-C*04:01 |
1.4597 |
| 382 | YIVVGRKDK | 6.4–6.6 | 0.92 | HLA-A*03:01; HLA-A*11:01;HLA-A*68:01 | 2.5185 |
| 394 | HHRHKAGST | 8.9–13.7 | 0.70 | HLA-B*07:02, HLA-B*14:02 | 0.5088 |
aPercentile score vary in allele specific manner. The lower the score better is the binding specificity [46]. The range of scores was obtained by setting cut off. bProteosomal cleavage score is the average of two kinds of scores: constitutively expressed type and INF-γ induced type. cAntigenic score was computed using Doytchinova and Flower's (2007) method [47]
Three score criteria were followed to screen the epitopes: MHC class I binding score, proteosomal cleavage score and antigenicity score. Association of HLA alleles for each epitope was determined by a cut off for percentile rank value ≤ 20.0. Epitopes were further checked for their efficacy in interactions at the peptide binding groove (see below)