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Table 4 Prediction of MHC class I specific peptide epitopes

From: Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India

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
  1. 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]
  2. 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)