Table 3 Benchmarking MHC class I predictors on recently published binding affinity data (HPV16), see also Table 4 for allele-wise scores
From: USMPep: universal sequence models for major histocompatibility complex binding affinity prediction
allele | mean AUC ROC | overall AUC ROC |
|---|---|---|
USMPep_FS_ens | 0.824(3) | 0.814(3) |
USMPep_FS_sng | 0.818(4) | 0.808(4) |
USMPep_LM_ens | 0.831(4) | 0.815(3) |
USMPep_LM_sng | 0.813(5) | 0.802(4) |
MHCFlurry | 0.817(4) | 0.809(4) |
NetMHC 3.4 | 0.831(3) | 0.794(3) |
NetMHC 4.0 | 0.803(4) | 0.780(3) |
NetMHCpan 2.8 | 0.818(4) | 0.792(3) |
NetMHCpan 3.0 | 0.815(4) | 0.787(3) |
NetMHCpan 4.0 | 0.820(3) | 0.792(4) |
SMM | 0.684(5) | 0.695(4) |
SMMPMBEC | 0.722(6) | 0.723(4) |
Pickpocket 1.1 | 0.760(5) | 0.708(4) |
consensus | 0.751(5) | 0.766(4) |
IEDB recommended | 0.756(5) | 0.772(4) |
NetMHCcons 1.1 | 0.827(4) | 0.799(3) |