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Figure 4
Schematic diagram of a connectivity conflict in the course of three-dimensional alignment. If SSE pairs (v11,v12) and (v41,v42) are matched by the three-dimensional graph-matching procedure then they are properly connected. If superposition of the structures shows that the C[_\alpha] atoms of SSE pairs (v21,v32) and (v31,v22) may also be mapped, the algorithm first tries to map atoms of a pair with minimal RMSD of na closest atoms (cf. text), (v31,v22) in the figure. These atoms may be mapped without a conflict. However, then atoms of SSE pair (v21,v32) cannot be mapped without breaking the connectivity (dashed line in the figure), and therefore these atoms remain unmapped.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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