Fig. 5: The advantage of hierarchical assembly over global AFM. | Nature Methods

Fig. 5: The advantage of hierarchical assembly over global AFM.

From: CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2

Fig. 5: The advantage of hierarchical assembly over global AFM.

a, Experimental structure of the early Pp module assembly intermediate of complex I (left) and the interaction graph (right). The node colors correspond to subunit colors. The edges are shown for all subunit pairs that have close contacting amino acids. Edges are labeled with the highest DockQ generated by AFM in the first stage of CombFold and their average PAE. b–d, Predicted models (top) with the quality of their pairwise interactions (DockQ, PAE) mapped on the interaction graph (bottom) for AFM (b), CombFold (c) and CombFold with crosslinks (d). Accurate pairwise interactions (DockQ >0.23) are in red. Crosslinks are shown as blue lines. CombFold assembly order is indicated on the graph with numbers in parentheses (blue).

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