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. Author manuscript; available in PMC: 2019 Sep 1.
Published in final edited form as: Biochim Biophys Acta Biomembr. 2018 Mar 14;1860(9):1687–1697. doi: 10.1016/j.bbamem.2018.03.011

Figure 3.

Figure 3

The network-based approach to identify β-barrel structures. (A) The schematic β-sheet contact network, where each element represents a peptide and any two peptides forming adjacent β-strands in a β-sheet is connected. The network is composed of two clusters with more than one connected elements (color in black and blue respectively) and isolated elements (colored in red). The circular structure highlighted by thick links represent a β-barrel structure. (B) By iteratively removing dangling elements (i.e., having only one contacted neighbors), the only structure left in addition to isolated elements (removed) is the circular β-barrel. (C, D) Schematics of possible multi-barrel structures where a peptide could form more than two β-sheet neighbors. In our simulations of short peptides, such cases were not observed.