Fig. 5

3D vector representations of amino acids as derived from the kernel matrices K ₁=BL62 and K ₁=BL62^β with β=0.2 (panels a and b, respectively), and from the optimized kernel matrices K ₁ for k _max =2 and k _max =10, (panels c and d, respectively). The proximity of these vectors relate to the chemical similarities of the amino acids they represent. To highlight this fact, we show the known polar amino acids (Q, R, E, K, N, D, T, H, and S) in red, the hydrophobic amino acids (M, V, L, I, P, and C) in blue, and the aromatic amino acids (Y, F, and W) in magenta. Note that the two small amino acids, A and G (shown in green), stand out