Skip to main content

Table 1 Algorithm for neoantigen prediction

From: The role of neoantigen in immune checkpoint blockade therapy

Algorithm Brief description of algorithm Refs.
NetMHC-3.0 Artificial neural network-based algorithm for prediction of binding affinity between MHC-I and peptides of length 8–11 [89]
NetMHCpan-3.0 Machine-learning model-based algorithm for prediction of binding affinity between MHC-I and peptides, a pan-specific version [90]
NetMHCcons Comprehensive algorithm for prediction of binding affinity between MHC-I and peptides [41]
NetMHCstab Artificial neural network-based algorithm for prediction of stability of peptide-MHC-I complex [91]
PickPocket Position-specific scoring matrix-based algorithm for prediction of binding affinity between MHC-I and peptides [92]
FRED2 Epitope prediction for neoantigen [93]
NetCTL-1.2 Comprehensive prediction algorithm containing proteasome cleavage, TAP transport, and MHC-I binding affinity [94]
NetCTLpan The pan-specific version of NetCTL [95]
NetTepi Integrated prediction algorithm containing binding affinity, stability of peptide-MHC-I complex, and T cell propensity [46]
pVAC-Seq Identification of neoantigen by tumor mutation and expression data [96]
EpiToolKit Prediction of MHC-I typing and T cell epitope [97]
WAPP Comprehensive prediction algorithm containing proteasome cleavage, TAP transport, and MHC-I binding affinity [98]
  1. MHC major histocompatibility complex, TAP transporter associated with antigen processing