Extended Data Fig. 6: Effects of loop resampling and optimization.
From: A backbone-centred energy function of neural networks for protein design
a, The distribution of the per-residue SCUBA energy changes of loop residues caused by loop resampling and optimization. For the H2E4 backbone structures, the changes were calculated as the energies after loop re-optimization minus the energies before loop re-optimization. b, The distribution of the lowest r.m.s.d. values (noted as RMSD in the figure) of predicted structures from designed structures. c, The distribution of per-residue Rosetta energy of the lowest-r.m.s.d. predicted structures. For b and c, the predictions were carried out using Rosetta biased forward folding for sequences designed from the loop re-optimized H2E4 backbone structures (thinner blue lines), or for sequences designed from H2E4 backbone structures not yet subjected to loop re-optimization (thicker red lines).
