(1) The use of regularly sized beads in the protein backbone cannot represent the tight packing required in secondary structures. Backbone-backbone intrachain distances are often already within the steep repulsive regime of the LJ potential of regular backbone beads (interaction between bead type P2-P2, which has a minimum distance at 0.528 nm, Figure ,A.). The impact of this is obvious when looking at the intrachain packing of secondary structures given the associated numerical and structural instabilities, particularly in α-helices and β-sheets, where most interaction distances are around 0.47 to 0.48 nm (Figure , B & C). While this may not seem like a large deviation from the LJ minimum, the steep repulsive regime in the LJ potential results in high forces, even for distances marginally smaller than the minimum. Currently, this issue is mitigated by the use of intramolecular exclusions and secondary structure biases, like the DSSP restrains or the OLIVES secondary network.