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 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
Consensus IEDB method 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 65 68 69 70 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.0 64 64 62 61 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NN-align 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
SMM-align 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
NetMHCIIpan-3.2 47 46 45 48 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.1 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
Tepitope (Sturniolo) 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 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 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
Consensus IEDB method 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 0 50 56 70 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.0 71 100 75 61 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NN-align 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
SMM-align 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
NetMHCIIpan-3.2 64 67 0 48 - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.1 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
Tepitope (Sturniolo) 36 - 13 22 - 68 22 25 38 0 27 10 50 7 - 0 30 29 0 - - - 40 15 10 - 60 - 52 - - 25
Comblib matrices - - 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.