Evaluating the Immunogenicity of Protein Drugs by Applying In Vitro MHC Binding Data and the Immune Epitope Database and Analysis Resource

Table 1

The MHC class II prediction tools available at IEDB. A user may choose from one of the seven prediction methods provided. The consensus method is used as the default method and is composed of three of the most successful individual prediction methods.

Methods	Prediction based on	Reference
Consensus	Combination of NN-align, SMM-align and CombLib	Wang et al., 2010 [38]
NetMHCIIpan	Artificial neural network	Nielsen et al., 2010 [31]
NN-align	Artificial neural network	Nielsen and Lund, 2009 [35]
SMM-align	Stabilization matrix alignment	Nielsen et al., 2007 [11]
Combinatorial library	Position scanning combinatorial libraries	Wang et al., 2008 [33]; Wang et al., 2010 [38]
Sturniolo	Scoring matrix based	Sturniolo et al., 1999 [39]
ARB	Average relative binding	Bui et al., 2005 [30]