Coordinates and potentials used for side chain interactions.

Top. For each residue, a reference backbone structure is aligned to the N, Cα, and C atomic coordinates. This alignment creates a reference frame to establish the position and direction of the side chain bead. The two side chain beads x1 and x2 for a pair of residues establishes three coordinates, the distance r and angles θ1 and θ2. Bottom. Example of distance-dependent potential, unif(r12), after training, between the side chain and backbone residues. These interactions cutoff at 5 Å while the side chain-side chain interactions cutoff at 7 Å. The thin lines describe the Vradial of oxygen (red) and hydrogen (blue), and the thick lines describe Vradial + Vangular for the same interactions.