Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
Fig 2
Flowchart of one iteration of the CE-Symm algorithm.
Algorithm steps are grey rectangles, inputs and outputs are blue rounded rectangles, decision rules are green rhomboid boxes and final classifications are orange hexagonal rectangles. Additional iterations on the resulting repeats may be performed to detect further symmetry axes or hierarchical symmetry. The images on the right represent, from top to bottom: a) initial structure, colored by secondary structure elements; b) self-alignment dot-plot matrix, where similarity score is a range from blue (high similarity) to magenta (low similarity), the identity alignment is blacked out and the optimal self-alignment path is in white; c) superposition of the structure against itself based on the optimal self-alignment, where the original structure is in blue and cyan and a copy of the structure is in yellow and orange (orange and cyan correspond to the regions of the alignment involving a circular permutation); d) subset of the alignment graph with seven connected components of six aligned residues each; e) superposition of the six internally symmetric repeats according to the symmetry axis (yellow bar) and their residue equivalencies; and f) structure inside the six-fold cyclic symmetry (C6) box, with repeats colored differently.