Figure 5.
Free energy funnels around the native structure. The energy ℰ and rmsd (A), the energy ℰ and the angular deviations θA0 (B), and δχ0 (C) are shown for a set of randomly perturbed structures of the protein–protein complex 1FIN. States of lower energy are seen to be associated with smaller angles, suggesting that the angles are a reasonable measure for the deviation from the correctly complexed structure. The two parallel lines represent the two energy cutoffs ℰc = ℰav and ℰc = ℰav − 5kT, where ℰav is the average energy of the five lowest energy complexes with an rmsd above 10 Å. The vertical lines in the plots indicate the resulting angular constraints θA0 and δχ0 corresponding to ℰc = ℰav (dashed line) and ℰc = ℰav − 5kT (dotted/dashed line).