Table S1. List of binding affinity data volume for each HLA ... - PLOS

 

Table S1. List of binding affinity data volume for each HLA Class I and II allele (9-mer and 15-mer respectively) benchmarked in this study. The test data were derived by subtracting the most recent version of training datasets included by the prediction tools from all quantitative MHC-ligand binding assay data curated in IEDB database (as of Oct. 2016). For HLA class II alleles, grey font entries represent alleles that have yet to be trained for IEDB tools and thus are excluded from the current benchmarking.

 

HLA Class I Allele

# of test data

% of strong binder (IC50 < 50 nM)

% of weak binder (50 nM < IC50 < 500 nM)

% of nonbinder (IC50 > 500 nM)

# of training data included by prediction tools

A*01:01 A*02:01 A*02:02 A*02:03 A*02:05 A*02:06 A*03:01 A*11:01 A*24:02 A*29:02 A*30:01 A*30:02 A*31:01 A*32:01 A*33:01 A*68:01 A*68:02 B*07:02 B*08:01 B*15:01 B*15:03 B*27:04 B*27:05 B*27:06 B*35:01 B*38:01 B*44:03 B*51:01 B*53:01 B*54:01 B*57:01 B*58:01

51 426 152 115 27 88 83 93 70 47 77 93 74 37 57 85 105 108 38 33 72 30 188 26 96 177 72 36 113 44 65 49

9.8 42.7 81.6 80.9 0 64.8 25.3 61.3 25.7 38.3 96.1 43 48.6 97.3 12.3 43.5 40 14.8 76.3 97 100 0 1.1 0 14.6 28.8 2.8 11.1 13.3 27.3 12.3 28.6

3.9 9.6 13.8 0 81.5 29.5 18.1 8.6 15.7 0 1.3 16.1 0 0 0 11.8 0 17.6 2.6 0 0 0 37.8 3.8 3.1 41.2 4.2 0 0 18.2 13.8 20.4

86.3 47.7 4.6 19.1 18.5 5.7 56.6 30.1 58.6 61.7 2.6 40.9 51.4 2.7 87.7 44.7 60 67.6 21.1 3 0 100 61.2 96.2 82.3 29.9 93.1 88.9 86.7 54.5 73.8 51

1409 5441 1980 2571 34 2680 2658 2431 1421 1066 1180 846 2113 645 1299 1631 2085 1792 1291 1951 448 1 856 2 1265 217 494 720 638 434 673 986

 

HLA Class II Allele

# of test data

% of strong binder (IC50 < 50 nM)

% of weak binder (50 nM < IC50 < 1000 nM)

% of nonbinder (IC50 > 1000 nM)

# of training data included by prediction tools

DPA1*01:03/DPB1*02:01 DPA1*01:03/DPB1*03:01 DPA1*01:03/DPB1*04:01 DPA1*01:03/DPB1*04:02 DPA1*02:01/DPB1*01:01 DPA1*02:01/DPB1*05:01 DPA1*03:01/DPB1*04:02 DPB1*01:01 DPB1*02:01 DPB1*03:01 DPB1*04:01 DPB1*04:02 DPB1*05:01 DPB1*14:01 DPB1*20:01 DQA1*01:01/DQB1*05:01 DQA1*01:02/DQB1*05:02 DQA1*01:02/DQB1*06:02 DQA1*01:04/DQB1*05:03 DQA1*02:01/DQB1*02:02 DQA1*03:01/DQB1*03:01 DQA1*03:01/DQB1*03:02 DQA1*04:01/DQB1*04:02 DQA1*05:01/DQB1*02:01 DQA1*05:01/DQB1*03:01 DQB1*02:01 DQB1*02:02 DQB1*03:01 DQB1*03:02 DQB1*04:02 DQB1*05:01 DQB1*05:02 DQB1*05:03 DQB1*06:02 DRB1*01:01 DRB1*03:01 DRB1*04:01 DRB1*04:04

354 164 807 38 496 556 512 100 164 99 105 99 100 164 164 606 164 477 164 164 49 514 518 535 486 100 94 133 126 99 93 93 94 98 875 863 881 369

5.6 17.7 5 0 4.2 4.1 5.1 10 12.8 24.2 4.8 8.1 17 7.9 7.9 3.3 4.9 8.6 2.4 1.8 12.2 0.4 2.7 1.5 27.2 2 1.1 21.8 1.6 7.1 3.2 1.1 0 11.2 30.3 12.3 20.2 14.9

16.1 32.3 20.6 26.3 25.4 17.8 18.9 46 44.5 37.4 30.5 28.3 41 22.6 26.2 11.7 29.3 33.3 26.2 21.3 26.5 17.9 20.5 19.8 36.2 44 18.1 32.3 32.5 45.5 36.6 28 27.7 45.9 35.9 18.5 34.5 38.5

78.2 50 74.5 73.7 70.4 78.1 76 44 42.7 38.4 64.8 63.6 42 69.5 65.9 85 65.9 58.1 71.3 76.8 61.2 81.7 76.8 78.7 36.6 54 80.9 45.9 65.9 47.5 60.2 71 72.3 42.9 33.8 69.2 45.3 46.6

1772 0 0 0 1832 1589 1793 0 0 0 0 0 0 0 0 1464 0 1776 0 0 0 1751 1711 1680 1881 0 0 0 0 0 0 0 0 0 13204 3685 4195 1856

 

  DRB1*04:05 DRB1*07:01 DRB1*08:01 DRB1*08:02 DRB1*09:01 DRB1*10:01 DRB1*11:01 DRB1*12:01 DRB1*13:02 DRB1*15:01 DRB1*16:02 DRB3*01:01 DRB3*02:02 DRB4*01:01 DRB5*01:01

 

692 847 14 821 647 165 802 813 866 906 123 635 811 721 712

7.1 22.9 7.1 20.6 14.7 53.3 20.9 3.2 23 19.2 13 3.9 6.2 9.6 14

30.5 33.5 14.3 31.2 34.9 41.8 26.4 28.5 26.4 32.7 64.2 15.4 16.3 27.6 34

62.4 43.6 78.6 48.2 50.4 4.8 52.6 68.3 50.6 48.1 22.8 80.6 77.6 62.8 52

3507 4046 0 3355 3613 0 4062 0 3405 3981 0 3102 0 3445 4058