IEDB Analysis Resource

MHC II Automated Server Benchmarks


This is a live ranking of MHC II servers based on performance, which continues to be reevaluated over time. The weekly IEDB releases are automatically checked for datasets large enough to add to the benchmarks. The benchmark metrics in the table below will only be updated on releases where such new data is becoming available.

Accumulated overall ranking scores

Ranking scores based on data sets submitted to the IEDB for the last at least 5 references.

Server 2023-04-21 2023-03-03 2023-01-27 2022-10-28 2022-09-16 2022-09-02 2022-06-17 2022-06-10 2022-04-08 2022-04-01 2021-12-10 2021-11-05 2021-10-29 2021-07-23 2021-04-23 2021-04-16 2021-02-19 2021-01-22 2020-12-18 2020-10-30 2020-10-23 2020-08-07 2020-06-26 2020-05-01 2020-03-27 2020-03-16 2020-01-03 2019-07-02 2019-05-24 2019-03-22 2018-11-23 2017-12-29 2017-11-24 2017-08-18 2017-06-30 2017-04-28 2017-04-11 2016-12-31
NetMHCIIpan-4.0 72 73 72 71 78 65 64 64 62 61 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.2 69 67 67 66 56 48 47 46 45 48 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.1 67 57 55 56 40 42 42 36 47 47 52 54 60 58 57 58 55 58 46 49 60 61 60 64 55 64 65 65 71 84 79 76 78 73 73 93 86 81
Consensus IEDB method 57 62 62 64 63 65 65 69 71 71 69 68 68 66 66 71 73 69 73 76 62 60 60 58 58 61 64 66 64 64 64 61 58 57 57 42 50 52
NN-align 2.3 50 50 51 50 48 63 65 68 69 70 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
SMM-align 47 49 45 47 44 49 51 48 48 45 51 51 53 49 51 43 43 43 57 61 57 57 54 56 38 41 43 39 43 49 35 31 34 36 36 44 49 45
NN-align 43 42 44 43 43 55 55 56 60 61 60 60 61 68 64 73 73 75 59 60 73 74 78 79 88 75 71 71 66 54 63 65 65 69 69 79 75 65
Tepitope (Sturniolo) 38 40 45 44 44 29 22 39 33 33 39 37 27 21 24 17 18 14 21 29 27 25 27 26 33 28 26 26 29 21 47 53 53 52 52 6 8 25
Comblib matrices 5 3 3 3 13 10 10 8 14 12 15 15 17 10 11 8 8 7 30 38 25 25 21 10 0 0 5 5 5 10 4 0 0 0 0 13 6 14


Weekly ranking scores

Ranking scores based on data sets submitted to the IEDB within a single week.

Server 2023-04-21 2023-03-03 2023-01-27 2022-10-28 2022-09-16 2022-09-02 2022-06-17 2022-06-10 2022-04-08 2022-04-01 2021-12-10 2021-11-05 2021-10-29 2021-07-23 2021-04-23 2021-04-16 2021-02-19 2021-01-22 2020-12-18 2020-10-30 2020-10-23 2020-08-07 2020-06-26 2020-05-01 2020-03-27 2020-03-16 2020-01-03 2019-07-02 2019-05-24 2019-03-22 2018-11-23 2017-12-29 2017-11-24 2017-08-18 2017-06-30 2017-04-28 2017-04-11 2016-12-31
NetMHCIIpan-4.0 71 100 100 68 76 79 71 100 75 61 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.2 71 57 79 69 62 50 64 67 0 48 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.1 100 86 57 65 31 36 86 42 56 39 33 24 63 63 49 100 - 61 50 41 - 100 0 61 88 75 - 25 51 83 90 67 100 - 75 - 63 81
Consensus IEDB method 43 29 21 62 72 43 71 42 44 68 50 83 71 63 61 25 85 68 50 88 - 38 90 62 25 50 - 75 64 57 90 83 50 - 60 - 38 52
NN-align 2.3 100 7 21 51 59 21 0 50 56 70 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
SMM-align 29 71 43 47 50 0 79 0 63 53 33 43 43 13 78 50 52 33 50 63 - 75 30 58 63 25 - 50 34 53 40 0 90 - 26 - 100 45
NN-align 0 43 36 47 32 79 21 50 94 54 83 52 66 100 44 75 54 84 50 69 - 38 60 77 88 100 - 100 83 53 60 67 40 - 69 - 75 65
Tepitope (Sturniolo) 14 7 43 42 41 100 36 - 13 22 - 68 22 25 38 0 27 10 50 7 - 0 30 29 0 - - - 40 15 10 - 60 - 52 - - 25
Comblib matrices - - - 5 0 - - - 50 5 - 0 23 0 12 - 13 10 - 0 - - 90 12 - 0 - 0 0 - 20 - 0 - 0 - 0 14


Download initial benchmark datasets

Click here to download the initial benchmark datasets.