Figure 3.
Scatter plot of the predicted score versus the measured binding affinity for the 528 peptides in the Buus data set. The figure shows the performance for four different prediction methods. The insert to each figure shows an enlargement of the part of the plot that corresponds to a binding affinity stronger than 500 nM. (A) Rammensee matrix method, (B) Hidden Markov Model trained on sequences in the Rammensee data set, (C) Neural Network trained with sparse sequence encoding, and (D) Comb-II neural network method. The straight line fit to the data in (C) and (D) have slope and intercept of 0.989, −0.029 and 0.979, −0.027, respectively.