Figure 1

Flexible Structural Alignment. The Figure shows proteins A and B which have 3 similar structure fragments. A rigid alignment (top right) is not able to align the blue fragment, but a flexible alignment (bottom right) can do this easily by introducing a hinge between the rigid block (the black and green fragments) and the blue fragment. As we assemble the alignment from well-aligned pairs, we introduce hinges to get a longer alignment and smaller rmsd.