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

Figure 9

Structural alignment of two cystatin-like folds: delta-5-3-ketosteroid isomerase from pseudomonas putida, PDB ID: 1opy (black) and chicken egg white cystatin, PDB ID: 1cewI (gray), obtained by (a) a heuristic method and (b) MaxPairs. For simplicity of presentation, we hide the parts of two structures that are not well superimposed by either program. In this particular test case, switching to MaxPairs superpositions yields a twofold increase in the number of pairs of residues that can be fit under 3 Å (59 versus 29). The corresponding percentage increase for the distance cutoff of 5 Å is 76% (65 versus 37 pairs).