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 2024-08-30 2024-04-19 2024-04-05 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-4.2 BA 82 74 74 73 73 74 68 70 70 70 76 68 68 63 65 65 65 64 69 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.3 BA 77 74 70 69 67 69 67 72 73 72 74 67 66 64 69 70 72 73 78 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.1 BA 75 75 77 79 84 82 70 69 67 67 68 63 64 66 64 64 66 65 63 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.0 BA 71 72 71 72 77 78 69 67 65 65 63 63 65 66 62 62 63 62 58 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.2 61 63 69 67 64 64 62 60 58 59 44 50 50 51 61 62 68 70 75 - - - - - - - - - - - - - - - - - - - - - - - - -
NN-align 2.3 59 46 57 56 54 58 51 48 47 47 41 62 62 66 67 67 65 67 66 - - - - - - - - - - - - - - - - - - - - - - - - -
NN-align 57 50 46 44 37 42 43 41 41 40 39 59 59 59 58 59 55 56 56 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
NetMHCIIpan-3.1 53 54 57 59 50 52 65 55 53 54 39 48 48 42 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
Consensus IEDB method 48 53 52 52 49 56 54 55 54 55 51 64 66 69 66 66 63 62 62 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
NetMHCIIpan-4.2 EL 35 43 38 38 43 38 50 54 56 57 56 38 40 37 40 41 42 40 43 - - - - - - - - - - - - - - - - - - - - - - - - -
SMM-align 35 44 38 41 42 43 51 49 46 47 39 55 55 52 50 47 51 52 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-4.0 EL 29 26 23 24 28 24 47 45 48 49 44 33 33 31 34 34 37 35 37 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.3 EL 29 32 30 31 38 35 49 51 53 52 50 37 37 36 35 35 33 32 32 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.1 EL 28 40 39 38 44 39 52 51 54 54 47 30 31 32 35 35 39 37 39 - - - - - - - - - - - - - - - - - - - - - - - - -
Tepitope (Sturniolo) 28 35 31 31 26 30 39 38 39 39 31 30 27 42 38 38 43 41 30 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 14 24 24 24 18 12 7 5 5 5 12 18 18 16 19 17 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


Weekly ranking scores

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

Server 2024-08-30 2024-04-19 2024-04-05 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-4.2 BA 86 62 100 77 40 79 50 86 86 68 72 79 82 77 97 64 75 52 69 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.3 BA 78 70 79 83 50 74 34 64 89 70 77 79 64 85 50 66 67 58 78 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.1 BA 80 61 64 68 33 89 71 100 96 67 64 71 71 96 57 60 88 71 63 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.0 BA 74 65 71 62 47 82 56 93 86 68 57 43 75 96 77 60 83 71 58 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-3.2 64 27 93 76 53 71 39 57 64 64 47 25 68 62 0 53 17 57 75 - - - - - - - - - - - - - - - - - - - - - - - - -
NN-align 2.3 67 16 57 55 40 56 100 32 25 51 46 11 14 54 57 69 17 72 66 - - - - - - - - - - - - - - - - - - - - - - - - -
NN-align 56 51 86 61 63 37 0 50 39 46 29 39 29 54 93 60 42 51 57 100 44 75 54 84 50 69 - 38 60 77 88 100 - 100 83 53 60 67 40 - 69 - 75 65
NetMHCIIpan-3.1 49 54 50 86 23 44 78 79 50 64 30 18 89 50 63 46 21 33 52 63 49 100 - 61 50 41 - 100 0 61 88 75 - 25 51 83 90 67 100 - 75 - 63 81
Consensus IEDB method 47 54 43 59 3 57 43 43 32 57 53 21 71 50 50 68 - 79 59 63 61 25 85 68 50 88 - 38 90 62 25 50 - 75 64 57 90 83 50 - 60 - 38 52
NetMHCIIpan-4.2 EL 30 72 21 13 100 40 55 21 14 53 68 68 54 4 20 39 92 32 43 - - - - - - - - - - - - - - - - - - - - - - - - -
SMM-align 29 61 29 38 47 41 14 71 43 52 38 0 75 27 63 58 8 43 45 13 78 50 52 33 50 63 - 75 30 58 63 25 - 50 34 53 40 0 90 - 26 - 100 45
NetMHCIIpan-4.0 EL 27 55 7 11 73 17 59 14 25 49 42 100 36 12 47 29 100 29 37 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.3 EL 28 55 0 9 83 31 58 7 46 51 57 75 14 8 53 37 63 31 32 - - - - - - - - - - - - - - - - - - - - - - - - -
NetMHCIIpan-4.1 EL 25 57 14 9 83 44 68 0 7 55 55 75 11 27 20 29 96 34 39 - - - - - - - - - - - - - - - - - - - - - - - - -
Tepitope (Sturniolo) 9 42 36 51 57 20 7 32 46 42 28 57 43 - 7 28 - 68 30 25 38 0 27 10 50 7 - 0 30 29 0 - - - 40 15 10 - 60 - 52 - - 25
Comblib matrices 10 23 - 37 3 23 - - - 7 0 - - - 47 15 - 7 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.


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