NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure

Table 5 LOO benchmark comparison of the pan-specific NetMHCIIpan-2.0 and the NetMHCIIpan-1.0 methods

The two methods are compared in a leave-one-out experiment on the peptide binding data described in the original NetMHCIIpan publication [29].
# is the number of peptide binding data for each allele, #bind is the number of peptides with a binding affinity stronger than 500 nM. NetMHCIIpan-1.0 is the method by Nielsen et al. [29], NetMHCIIpan-2.0 is the method described here, and TEPITOPE is the method by Sturniolo et al. [1]. Prediction values for NetMHCIIpan-1.0 were taken from [29]. Ave gives the per allele average, Ave* gives the per allele average of the 11 alleles characterized by the TEPITOPE method. In bold is highlighted the best performing method for each of the 14 alleles. AUC values were calculated using a binding threshold of 500 nM. Only AUC values are included for the TEPITOPE method since prediction values for this method are not linearly related to the binding affinity.