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 2023-11-10 2023-09-01 2023-07-28 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-4.1 BA 80 85 82 70 71 70 70 76 65 65 65 65 65 67 66 65 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.0 BA 73 76 78 68 70 68 68 70 65 66 66 63 63 63 62 61 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.2 68 67 67 64 65 64 63 52 51 51 50 61 63 69 70 77 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.1 61 53 54 66 56 54 55 41 47 47 41 46 46 48 50 54 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
NN-align 2.3 58 56 59 51 49 49 48 45 63 64 67 67 67 65 67 67 - - - - - - - - - - - - - - - - - - - - - - - - -
Consensus IEDB method 53 50 58 58 59 59 61 57 66 66 68 65 66 63 62 63 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 44 38 42 44 43 43 42 43 58 58 57 57 59 55 56 57 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 40 43 42 50 50 47 48 42 55 56 52 50 47 50 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-4.1 EL 38 45 39 51 54 57 57 54 32 32 33 36 36 38 36 38 - - - - - - - - - - - - - - - - - - - - - - - - -
Tepitope (Sturniolo) 30 26 30 39 39 41 41 37 31 27 41 36 37 41 39 29 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 24 20 14 7 4 4 4 13 17 17 15 18 16 16 16 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
NetMHCIIpan-4.0 EL 22 27 24 47 47 50 51 48 31 31 29 34 33 37 34 38 - - - - - - - - - - - - - - - - - - - - - - - - -


Weekly ranking scores

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

Server 2023-11-10 2023-09-01 2023-07-28 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-4.1 BA 70 41 89 70 100 100 66 75 85 75 94 55 62 89 67 65 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.0 BA 63 50 83 45 90 90 69 66 55 80 94 82 62 83 66 61 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.2 76 59 75 35 60 75 67 58 35 70 67 0 53 28 52 77 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.1 88 32 47 80 80 55 65 31 25 90 50 64 44 22 31 53 63 49 100 - 61 50 41 - 100 0 61 88 75 - 25 51 83 90 67 100 - 75 - 63 81
NN-align 2.3 55 50 59 100 25 25 51 52 15 10 56 59 71 28 68 67 - - - - - - - - - - - - - - - - - - - - - - - - -
Consensus IEDB method 58 5 59 50 40 30 61 61 30 75 50 50 69 28 77 60 63 61 25 85 68 50 88 - 38 90 62 25 50 - 75 64 57 90 83 50 - 60 - 38 52
NN-align 60 73 37 0 50 40 47 32 55 25 56 95 58 44 49 58 100 44 75 54 84 50 69 - 38 60 77 88 100 - 100 83 53 60 67 40 - 69 - 75 65
SMM-align 33 55 41 20 70 45 51 43 0 80 17 68 59 17 42 44 13 78 50 52 33 50 63 - 75 30 58 63 25 - 50 34 53 40 0 90 - 26 - 100 45
NetMHCIIpan-4.1 EL 5 91 44 70 0 10 54 65 85 10 17 23 32 94 31 38 - - - - - - - - - - - - - - - - - - - - - - - - -
Tepitope (Sturniolo) 46 64 20 10 25 50 42 34 70 45 - 9 27 - 67 27 25 38 0 27 10 50 7 - 0 30 29 0 - - - 40 15 10 - 60 - 52 - - 25
Comblib matrices 32 5 26 - - - 7 0 - - - 50 13 - 5 24 0 12 - 13 10 - 0 - - 90 12 - 0 - 0 0 - 20 - 0 - 0 - 0 14
NetMHCIIpan-4.0 EL 5 77 17 55 10 30 49 50 100 35 0 45 28 100 25 38 - - - - - - - - - - - - - - - - - - - - - - - - -


Download initial benchmark datasets

Click here to download the initial benchmark datasets.


Benchmark results get recalculated as new servers are added to the benchmarks. Numbers in light grey represent scores on datasets before the server was incorporated into the benchmarks. Previous versions of the benchmark results can be downloaded below