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Fig. 6 | Algorithms for Molecular Biology

Fig. 6

From: Quantifying steric hindrance and topological obstruction to protein structure superposition

Fig. 6

Left: the alpha carbon trace of CATH domain 1emd01 and its self-intersection free interpolation with its smoothened black curve. Center and right: the interpolation between CATH domains 1csgA0 and 1jli00 alpha carbon and smoothened curves respectively. The two domains share the homology-class 1.20.120.200. Both interpolations have one self-intersection indicated by a black face. In both cases it may be circumvented by a large \(\Omega _1\) move. If the user does not allow such large rearrangements, this self-intersection is called essential and the size of an end-contraction avoiding it is calculated. As the alpha carbon RMSD is 5.6Å this is an example that a change in topology that seems to demand quite different folding pathways may happen for a smaller RMSD and for homologous chains

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