From: Immunoinformatics and epitope prediction in the age of genomic medicine
Predictor/tool | Key method | Reference |
---|---|---|
HLA class I binding | ||
 Allele-specific | ||
  SYFPEITHI | PSSM | [14] |
  RANKPEP | PSSM | [27] |
  BIMAS | PSSM | [28] |
  SVMHC | SVM | [7] |
  netMHC | ANN | [29] |
 Pan-specific | ||
  MULTIPRED | HMM/ANN | [39] |
  netMHCpan | ANN | [40] |
  PickPocket | PSSM | [41] |
  TEPITOPEpan | PSSM | [42] |
  ADT | Threading | [43] |
  UniTope | SVM | [44] |
  KISS | SVM | [45] |
HLA class II binding | ||
 Allele-specific | ||
  SYFPEITHI | PSSM | [14] |
  netMHCII/SM-align | PSSM/ANN | |
  ProPred | PSSM | [50] |
  RANKPED | PSSM | [27] |
  TEPITOPE | PSSM | [51] |
  SVRMHC | SVM | [8] |
  MHC2MIL | Multi-instance learning | [52] |
  MHC2pred | SVM | – |
 Pan-specific | ||
  MULTIPRED | HMM/ANN | [39] |
  MHCIIMulti | Multi-instance learning | [55] |
  TEPITOPEpan | PSSM | [42] |
  netMHCIIpan | ANN | |
 Consensus methods | ||
  CONSENSUS | – | [57] |
  netMHCcon | – | [56] |
 Binding stability | ||
  netMHCstab | ANN | [47] |
Proteasomal cleavage | ||
  in vitro | ||
  netChop 20S | ANN | [60] |
  PCM | PSSM | [61] |
  FragPredict | PSSM | [62] |
  Pcleavage | SVM | [63] |
  PAProC | ANN | [64] |
  in vivo | ||
  netChop Cterm | ANN | [60] |
  ProteaSMM | PSSM | [65] |
TAP transport | ||
 PredTAP | HMM/ANN | [39] |
 SVMTAP | SVM | [61] |
Integrated processing | ||
 EpiJen | – | [70] |
 WAPP | – | [61] |
 NetCTL | – | [71] |
 NetCTLpan | – | [72] |
T-cell reactivity | ||
 POPI | SVM | [74] |
 POPISK | SVM | [75] |
B-cell epitope prediction | ||
 Continuous | ||
  COBEpro | SVM | [78] |
  BCPRed | SVM | [79] |
  FBCPred | SVM | [79] |
 Discontinuous | ||
  EPMeta | SVM | [82] |
  Discotope 2.0 | Linear regression | [83] |
NGS-based HLA typing | ||
 ATHLATES | Contig assembly | [25] |
 seq2HLA | Greedy algorithm | [26] |
 OptiType | Integer linear programming | [19] |
 Polysolver | Bayesian classification | [20] |