Optimize prediction sensitivity by following our recommendations:

Based on a dataset comprised of >750 experimentally validated MHC-peptide binding affinities for the proteins HPV16 E6 and HPV16 E7, we evaluated the performance of all prediction servers included in MHCcombine.
The detailed results of our analysis can be accessed via:

M. Bonsack, S. Hoppe, J. Winter, D. Tichy, C. Zeller, M. D. Küpper, E. C. Schitter, R. Blatnik, A. B. Riemer

Performance Evaluation of MHC Class-I Binding Prediction Tools Based on an Experimentally Validated MHC-Peptide Binding Data Set.

Cancer Immunology Research (2019) PMID: 30902818

Please note:
NetMHCpan 4.1 was published after our analysis and is therefore not contained in our recommendations table.

We would recommend to use the following servers for the following purposes:

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 NetMHCpan 4.0 NetMHC 3.4 NetMHCpan 4.0 NetMHC 3.4 NetMHCpan 4.0
HLA-A2 NetMHCpan 4.0 NetMHC 4.0 NetMHCpan 4.0 IEDB SMMPMBEC NetMHC 4.0
HLA-A3 NetMHC 3.4 NetMHC 4.0 NetMHC 3.4 IEDB recommended IEDB SMMPMBEC
HLA-A11 IEDB recommended NetMHCpan 4.0 NetMHC 4.0 IEDB recommended IEDB recommended
HLA-A24 NetMHCcons 1.1 NetMHCpan 4.0 NetMHCpan 4.0 NetMHCcons 1.1 IEDB recommended
HLA-B7 NetMHCcons 1.1 IEDB recommended IEDB recommended NetMHCpan 3.0 NetMHC 3.4
HLA-B15 NetMHCpan 4.0 NetMHCpan 3.0 NetMHCpan 3.0 NetMHC 4.0 NetMHCpan 4.0

We found that many peptides are missed applying the thresholds recommended by the servers. To increase prediction sensitivity we recommend using the following more tolerant thresholds. Click on the prediction method to expand a table of thresholds.

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 6706nM 11702nM 6706nM 3676nM 6323nM
HLA-A2 6937nM 9129nM 1812nM 2566nM 11451nM
HLA-A3 6962nM 10605nM 3476nM 1603nM 234nM
HLA-A11 9342nM 9342nM 9086nM 1928nM 9183nM
HLA-A24 13918nM 25903nM 7820nM 9078nM 20604nM
HLA-B7 13279nM 21900nM 6674nM 8988nM 13279nM
HLA-B15 6476nM 14126nM 2652nM 6140nM 6525nM

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 9154nM 2008nM 5319nM 3631nM 11458nM
HLA-A2 6045nM 6045nM 7890nM 4749nM 4362nM
HLA-A3 3086nM 752nM 3086nM 2536nM 955nM
HLA-A11 6972nM 1354nM 13066nM 5497nM 6972nM
HLA-A24 12453nM 7863nM 6548nM 14977nM 17668nM
HLA-B7 11903nM 16001nM 5180nM 5373nM 14182nM
HLA-B15 5050nM 2654nM 3786nM 4551nM 438nM

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 8641nM 14781nM 3127nM 1548nM 8915nM
HLA-A2 8103nM 11632nM 4258nM 2254nM 12699nM
HLA-A3 1365nM 12511nM 8302nM 1365nM 132nM
HLA-A11 7720nM 7720nM 7399nM 2783nM 5361nM
HLA-A24 14268nM 33856nM 12844nM 12098nM 22982nM
HLA-B7 14911nM 5515nM 14911nM 5644nM 17527nM
HLA-B15 6790nM 7695nM 4782nM 7669nM 5189nM

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 7097nM 15251nM 1900nM 2246nM 2745nM
HLA-A2 9681nM 9488nM 4734nM 2033nM 11935nM
HLA-A3 5534nM 10537nM 8408nM 1769nM 163nM
HLA-A11 7709nM 5309nM 980nM 1722nM 7709nM
HLA-A24 12346nM 34571nM 12346nM 11145nM 18253nM
HLA-B7 14473nM 6605nM 6431nM 13277nM 14473nM
HLA-B15 7817nM 7375nM 4008nM 7103nM 3766nM

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 5684nM 2191nM 2318nM 268nM 5158nM
HLA-A2 4923nM 2302nM 8538nM 4923nM 4715nM
HLA-A3 2366nM 637nM 7002nM 2366nM 132nM
HLA-A11 7354nM 349nM 6918nM 5277nM 7182nM
HLA-A24 14229nM 10003nM 10229nM 12415nM 19060nM
HLA-B7 4553nM 1846nM 3666nM 3231nM 4553nM
HLA-B15 6047nM 2808nM 6047nM 10190nM 709nM

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 7693nM 2100nM 3511nM 4552nM 7693nM
HLA-A2 5383nM 2328nM 8572nM 8712nM 5383nM
HLA-A3 2000nM 693nM 4651nM 2000nM 355nM
HLA-A11 7734nM 686nM 6830nM 4407nM 7093nM
HLA-A24 13142nM 10028nM 10934nM 14565nM 20590nM
HLA-B7 7946nM 1092nM 4336nM 4175nM 7946nM
HLA-B15 5183nM 3220nM 5531nM 10875nM 558nM

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 5211nM 5211nM 1766nM 4289nM 7776nM
HLA-A2 954nM 736nM 561nM 705nM 954nM
HLA-A3 2874nM 1551nM 1655nM 4990nM 1423nM
HLA-A11 4063nM 3237nM 2417nM 4626nM 6683nM
HLA-A24 5045nM 5100nM 1655nM 5211nM 24219nM
HLA-B7 2874nM 2340nM 462nM 1585nM 1766nM
HLA-B15 6756nM 3933nM 4831nM 10875nM 2444nM

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 rank: 0.95 rank: 11.25 rank: 2.40 rank: 1.30 rank: 2.95
HLA-A2 rank: 10.35 rank: 1.00 rank: 14.00 rank: 6.60 rank: 16.05
HLA-A3 rank: 6.65 rank: 3.45 rank: 2.70 rank: 3.50 rank: 6.65
HLA-A11 rank: 8.85 rank: 11.05 rank: 5.70 rank: 6.15 rank: 8.85
HLA-A24 rank: 7.45 rank: 6.20 rank: 3.15 rank: 5.35 rank: 19.90
HLA-B7 rank: 4.15 rank: 17.90 rank: 2.50 rank: 3.50 rank: 1.10
HLA-B15 rank: 5.80 rank: 3.60 rank: 8.20 rank: 14.75 rank: 0.90

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 rank: 0.70 rank: 11.20 rank: 2.15 rank: 1.05 rank: 2.90
HLA-A2 rank: 9.25 rank: 0.80 rank: 8.70 rank: 6.20 rank: 9.25
HLA-A3 rank: 11.35 rank: 3.15 rank: 2.90 rank: 11.35 rank: 6.60
HLA-A11 rank: 7.45 rank: 10.65 rank: 5.00 rank: 4.85 rank: 7.45
HLA-A24 rank: 7.55 rank: 3.85 rank: 2.80 rank: 5.00 rank: 21.95
HLA-B7 rank: 4.20 rank: 17.85 rank: 2.50 rank: 3.80 rank: 1.30
HLA-B15 rank: 5.80 rank: 2.80 rank: 8.20 rank: 4.55 rank: 0.10

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 1042nM 3764nM 3601nM 1042nM 526nM
HLA-A2 1715nM 927nM 3073nM 1294nM 284nM
HLA-A3 1881nM 21976nM 1881nM 971nM 692nM
HLA-A11 1966nM 3425nM 1254nM 2716nM 510nM
HLA-A24 1854nM 1123nM 2183nM 3620nM 9957nM
HLA-B7 1085nM 3197nM 1085nM 667nM 4567nM
HLA-B15 478nM N/A 2911nM 354nM N/A

pooled (8-11-mers) 8-mers 9-mers 10-mers 11-mers
HLA-A1 315nM 16632nM 300nM 1754nM 2839nM
HLA-A2 1277nM 167nM 3077nM 1643nM 91nM
HLA-A3 2930nM 13611nM 1909nM 907nM 3706nM
HLA-A11 1539nM 3250nM 3634nM 2924nM 229nM
HLA-A24 3035nM 60nM 1725nM 3356nM 8672nM
HLA-B7 334nM 334nM 923nM 1327nM 88nM
HLA-B15 184nM N/A 1615nM 183nM N/A