Figure 4

Distinctive results of two simulation methods involving the predicted contacts: de novo folding and refinement. Results of de novo folding (a) are represented by the best model of the T0248-1 target superimposed on the native structure (RMSD = 2.3 Å) and by the contact map with depicted real and quite accurate and precisely predicted contacts (upper triangle) and contacts of the best model obtained in the folding simulation and the first model of the Kolinski-Bujnicki group (lower triangle). Significant improvement of model quality and its contact map with respect to the native is observed. Results of the refinement simulations (b) are represented by the best model of the T0215 target (green) superimposed on the native structure (blue) (RMSD = 5.5 Å) and by the contact map constructed in the same fashion as in (a). Despite the low quality of the contact data predicted for the T0215 target the quality of the final refined model improved (but not significantly) in comparison to the original Kolinski-Bujnicki results (RMSD = 7.9 Å from the crystallographic structure Cα-trace).