Figure 1

The two-bead model of protein structure is presented. Each residue consists of a Cα bead (grey) and a Cβ bead (white). Cα beads are placed at the position of the Cα atoms and form the backbone through being connected by virtual peptide bonds with a torsion angle φ. Each Cα bead (except Gly) binds a Cβ bead with a bond length b and bond angle θ. Cβ beads, whose centers reside at the geometric centroid of the residue atoms, are separated by a distance r_ij and have a radius r_i (proportional to the radius of gyration of the side chain atoms).