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Heuristic energy-based cyclic peptide design

Fig 8

Molecular dynamics simulation results of top designs.

(a) Backbone -atom RMSDs are calculated between the MD trajectory frames and our designed structures. Snapshots are shown for selected time points (designed structures in red, trajectory frames in blue). (b) REMD free energy surfaces. From the lowest free energy basins (marked by green boundaries), representative structures (colored in blue) are extracted from the histogram bins and aligned against our designed structures (red), with the population percentages in the minima labeled aside. The designed sequences are listed on the side.

doi: https://doi.org/10.1371/journal.pcbi.1012290.g008