Figure 4
From: Protein structure prediction by all-atom free-energy refinement
Top Row: Overlay of some predicted structures. The overlay of the predicted (red) and experimental conformation (green) documents the close agreement of conformations for 1orc[66] and 1ail[67]; only the backbone of the proteins is shown for clarity (generated with PYMOL [62]). Bottom row: Cβ-Cβ distance difference matrices: A pixel in row i and column j of the color coded distance map indicates the difference in the Cβ-Cβ distances of the native and the folded structure. Black (gray) squares indicate that the Cβ-Cβ distances of the native and the other structure differ by less than 1.5 (2.25)Å respectively. White squares indicate larger deviations. The data indicates clearly the presence of all short-range and long-range native contacts for the high-quality decoys and good agreement even for the predictions from low-quality decoy sets.