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Heuristic energy-based cyclic peptide design

Fig 5

Stability analysis of 15-residue designs.

(a) Correlation plot between values calculated by Rosetta simple_cycpep_predict and by our ClusterGen (left). The values of our ClusterGen are also plotted against the backbone root-mean-square radii (right). (b) Energy landscape comparison for one case in which both methods obtain high values. (c) Energy landscape comparisons for three cases in which the two methods calculate significantly different values. (d) Top designs with bending backbones. The backbone atoms, prolines (in color purple), and hydrophobic amino acids (ALA, ILE, LEU, VAL, MET, PHE in color orange) are shown. The backbone turn segments are enlarged. (e) Top designs with short alpha helices and consecutive i , i + 2 ∕ i + 3 H-bonds. The designed sequences are written in one-letter codes, with uppercase for L-amino acids, and lowercase for D-amino acids.

doi: https://doi.org/10.1371/journal.pcbi.1012290.g005