BioMed Research International / 2013 / Article / Fig 10

Research Article

On the Difference in Quality between Current Heuristic and Optimal Solutions to the Protein Structure Alignment Problem

Figure 10

Structural superposition of the urease from Bacillus pasteurii, PDB ID: 1ubpA (black) and the dynein light chain 1 from human, PDB ID: 1cmiA (gray), obtained by (a) a heuristic method and (b) MaxPairs (we hide misaligned C-terminal regions from both structures). In this test case, a subtle change in structural superposition, made by MaxPairs, increases the number of pairs of residues that can be fit under 3 Å from 9 to 36 (and from 16 to 42 when the cutoff distance of 5 Å is used).

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