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Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction

Figure 2

Local structural motifs used to model protein secondary structure as defined by the knob-socket model.

On the top for each type of secondary structure, ribbon diagrams of the protein backbone with black spheres at Cα positions are presented. On the bottom, two-dimensional lattice representations are shown of the local residue interactions that define secondary structure, where solid lines represent covalent contacts between residues and broken lines are packing interactions. Because only the local interactions are being considered to predict secondary structure, only the socket portion of the knob-socket model is used. The knob portion signifies interactions at the level of tertiary structure or packing of non-local residues distant in the protein sequence. Each of the 4 types of secondary structure are described in more detail. (a) Helix Model: Relative residue positions and interactions are shown. Two types of sockets are represented in different grey scale: sockets in dark grey and sockets in light grey. (b) Strand Model: Double-side sheet sockets are shown. Sockets and in white are facing one direction, a socket in dark grey faces the other side. Also, the side chain only socket is shown in light grey. (c) Coil Model: Three types of coil sockets are shown. The socket is closed socket with all three residues in contact one another, the socket is open socket with contact and contact but no contact between and , and the socket is strained socket with no contact between and . (d) Turn Model: Three residue sockets , , , and in the 5 residue turn are shown.

Figure 2