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Table 3 A comparison of peptide binding register prediction results for the peptide-MHC complexes listed in Table 5 using RTA and seven other prediction methods

From: Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

   Prediction Method
Class II MHC allotype PDB
entry
RTA ARB MHC2Pred NN-align ProPred RANKPEP SMM-align SVRMHC
DRB1*0101 1AQD
  1DLH NA NA
  1KLG
  1KLU
  1SJE
  1T5W
  2FSE NA NA
DRB1*0301 1A6A NA
DRB1*0401 1J8H NA NA
  2SEB NA NA
DRB1*1501 1BX2
DRB3*0101 2Q6W NA NA NA NA NA
DRB5*0101 1FV1
  1H15 NA NA
H2-IAb 1LNU NA NA NA NA
  1MUJ NA NA
H2-IAd 1IAO NA NA
  2IAD NA NA
Total correct   17/18 8/11 4/17 14/18 14/14 10/17 7/11 6/12
  1. "✔" indicates a correct prediction and "✘" indicates an incorrect one. "NA" denotes that a prediction is not available either because the method does not have a prediction model for that MHC type or the method cannot be applied to a peptide shorter than 15 residues.