Figure 1.

An example CRF model for protein conformation sampling. In this example, s_i (i.e., the label at position i) depends on the residues and secondary structure types at positions i−2, i−1, i, i+1, and i+2 and any nonlinear combinations of them. There is also interdependence between two adjacent labels. This CRF model can also be extended to incorporate long-range interdependence between two labels.