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).