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Table 2 Results from varying substitution matrices

From: Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores

AAindex reference Substitution matrix Best β Acc. AROC AROC50 MCC
HENS920102 BLOSUM62. Matrix based on possible pair-wise substitutions from aligned segments of polypeptides [34] 0.05 0.8049 0.8708 0.532 0.543
BLAJ010101 Matrix built from structural superposition data for identifying potential remote homologues [52] 0.027 0.8207 0.8752 0.540 0.571
DOSZ010104 SM_THREADER_NORM. Amino acid similarity matrices based on force fields (Normalised version) [36] 0.045 0.8217 0.8753 0.548 0.572
  1. Evaluating performance for using different scoring matrices using 10-fold CV. The test measurements are same as in previous experiment. Best values are shown in bold.