Here is an example - 1JPS.pdb, T chain

Epitopes as predicted by polynomial and RBF kernel:

Using Polynomial Kernel

GKDNTE
148 149 150 171 172 174
YKSSSSGKKTAKDKGEN
156 159 160 161 162 163 164 165 166 167 168 169 180 181 182 183 184

Using RBF Kernel

GKDNTE
148 149 150 171 172 174
YKSSSSGKKTAKDKGEN
156 159 160 161 162 163 164 165 166 167 168 169 180 181 182 183 184

Epitopes as visualized in Jmol-