Figure 2

Illustration of the DBN model. (a) An example of PSSM, where rows represent residue sites and columns represent amino acids. The "SS" column contains the secondary structure of each site, classified as H (helix), E (sheet), and C (coil). (b) A graphical representation of the DBN. The shadow nodes represent observable random variables, while clear nodes represent hidden (in prediction) variables. The arcs with arrows represent dependency between nodes. The contents of the nodes R _i , AA _i , d _i , and SS _i are derived as illustrated by the connections of dashed lines, where the subscript indicates the residue site. More detailed description of R _i , AA _i , d _i , SS _i , D _i , and F _i can be found in the text. L _AA and L _SS are windows sizes for profile and secondary structure, respectively (in this example, L _AA = 4 and L _SS = 2). (c) Is a reduced version of (b) with L _AA = 0 and L _SS = 0.