Figure 3

Obtaining the fast non-bijective correspondence: The Cα atom corresponding to each Cα atom of protein A is the nearest Cα atom in protein B. (a) Given the distance d₁ between Cα atoms 1A and 1B, (b) the Cα atom of B nearest to 1A is necessarily in the sphere of radius 2d₁ centered in 1B. With an ordered distance matrix for B, only a few distances need to be computed in practice.