Figure 2.

Showing the variation of the basin RMSD from crystal structure with the size of protein, (N_seq). We show the results for all 280 domains studied here: domains from α, β, α/β and α+β topological classes are colored black, red, green and blue, respectively. Here we consider the three most probable basins for each protein, RMS_A, RMS_B and RMS_C (see Fig. 1b). In (a) we show the RMSD value of the least native-like of the top three dominant energy basins (max(RMS_A,RMS_B,RMS_C)) as a function of the number of residues. One third of the domains (88 out of 280, 31.4 %) have RMSD values above 6 Å (dashed black horizontal line). On average α/β and β domains remain closer to the native state than other classes of domains. Only 4.29 % of proteins have RMSD values below 2 Å (dashed black horizontal line). 90 % of all-α, all-β, α/β and α+β class domains are below thresholds of 12.7 Å, 8.5 Å, 6.9 Å and 12.0 Å, respectively. In (b) we show the RMSD value of the most dominant energy basin (RMS_A) as a function of the number of residues. In this case, only 19.3 % (54 out of 280) of the domains have RMSD values above 6 Å (dashed black horizontal line) and almost all (66 out of 70 or 94.3 %) α/β domains are below the 6 Å line. 90 % of all-α, all-β, α/β and α+β class domains are below thresholds of 9.1 Å, 4.8 Å, 5.0 Å and 9.2 Å, respectively.