Figure 2

Intersection of sister lists. Complex 1 resulted from docking μ _i against μ _j , i, j ∈ [1...m]. Complex 2 resulted from docking μ _j against μ _i . μ _i is represented as a cross with an arrowhead; μ _j as a cross with a bulb. The different shades of gray are used to distinguish instances of the same model. In this case, if we align the two complexes by superimposing both instances of μ _i , then the distance between the centers of the two instances of μ _j is less than or equal to the cutoff, d_c, so both complexes are retained. Note that the instances of μ _j are not superimposed; only their centers coincide. Here, μ _i is the aligned model and μ _j is the orientation-independent model. When we align the two complexes by superimposing both instances of μ _j , then the distance between the centers of μ _i is greater than the cutoff. However, once a complex is retained, it is never again rejected.