Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

Krissinel, E.; Henrick, K.

doi:10.1107/S0907444904026460

Acta Crystallographica Section D
Acta Crystallographica
Section D BIOLOGICAL CRYSTALLOGRAPHY

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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 n_a 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.

BIOLOGICAL
CRYSTALLOGRAPHY

ISSN: 1399-0047

Volume 60| Part 12| November 2004| Pages 2256-2268

doi:10.1107/S0907444904026460

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