Figure 5. Top-ranked predicted structures can make correct contacts in the absence of constraints and avoid incorrect contacts in spite of false positive constraints.

The top blindly ranked structures are evaluated in terms of quality of contact prediction (N_C = 40 for Elav4, N_C = 130 for Ras, N_C = 160 for Trypsin). The predicted constraints (red stars) are correct when they coincide with contacts derived from the observed structure (grey circles) and otherwise incorrect (false positives, red on white). The contacts derived from the predicted 3D structure (dark blue) are in good general agreement with those from the observed structure (grey). The cooperative nature of the folding prediction process permits favorable situations, in which contacts regions not touched by a predicted constraint (red) are still predicted correctly (black circle for RAS, dark blue on grey, no red) and false positive constraints are not strong enough to lead to incorrect contacts (left black circle Elav4, red star, no dark blue or grey). However, in unfavorable situations missing constraints may imply that contact regions are fully or partially missed (black circle, trypsin) or mostly missed (right black circle for Elav4, grey adjacent to and wider than dark blue).