Figure 8
From: Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets
Contour representations of the interaction parameters for selected energy functions. Top row: energy functions with two, three and four amino acid classes, optimized for interface recognition using Optimization Set 2. Bottom row: six- and 20-class functions optimized over OS1 or OS2, as indicated. Contours levels in kcal/mol. Each energy matrix has a mean of zero. The amino acids belonging to each class are shown next to the corresponding rows and columns of each matrix. For the sake of clarity, the rows and columns of the 20-class matrix are not labelled individually but groupwise.