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 2020-12-18 2020-10-30 2020-10-23 2020-08-07 2020-06-26 2020-05-01 2020-03-27 2020-03-16 2020-01-02 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 66 68 60 58 59 58 58 61 64 66 64 64 64 61 58 57 57 42 50 -
NN-align 54 55 67 68 72 79 88 75 71 71 66 54 63 65 65 69 69 79 75 -
SMM-align 52 54 54 54 51 56 38 41 43 39 43 49 35 31 34 36 36 44 49 -
Tepitope (Sturniolo) 44 49 40 38 40 26 33 28 26 26 29 21 47 53 53 52 52 6 8 -
Comblib matrices 23 30 21 21 19 10 0 0 5 5 5 10 4 0 0 0 0 13 6 -
NetMHCIIpan-3.1 - 47 - - - - 55 64 65 65 71 84 79 76 78 73 73 93 - -


Weekly ranking scores

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

Server 2020-12-18 2020-10-30 2020-10-23 2020-08-07 2020-06-26 2020-05-01 2020-03-27 2020-03-16 2020-01-02 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 50 88 - 38 60 62 25 50 - 75 64 57 90 83 50 - 60 - 38 52
NN-align 50 69 - 38 46 77 88 100 - 100 83 53 60 67 40 - 69 - 75 65
SMM-align 50 63 - 75 36 58 63 25 - 50 34 53 40 0 90 - 26 - 100 45
Tepitope (Sturniolo) 50 7 - 0 74 29 0 - - - 40 15 10 - 60 - 52 - - 25
Comblib matrices - 0 - - 45 12 - 0 - 0 0 - 20 - 0 - 0 - 0 14
NetMHCIIpan-3.1 - 41 - 100 34 - 88 75 - 25 51 83 90 67 100 - 75 - 63 -


Download initial benchmark datasets

Click here to download the initial benchmark datasets.