Figure 3

Contact maps presenting results of fold-refinement simulations. The contact maps of the selected CASP6 targets are presented in (a). In the upper triangle in each contact map real (red) and predicted (green) contacts are compared. In the bottom triangle a contact map of Kolinski-Bujnicki's first model (blue) is superposed on a contact map of the final model obtained after the refinement simulations (grey). In most cases we observed improvement of the contact maps for models after the refinement. Some accurate contacts were rebuilt by the CABS despite not being preliminarily predicted (T0209-2). Some falsely predicted contacts in diffused clusters were not observed in the final model (T0281). Predicted contacts in dense and numerous clusters were observed almost in all cases (A and A' in the T0272-1 contact map), contrary to diffuse sparse contact clusters. (b) Lower triangles, contact maps of the T0272-1 models obtained after the simulations with restraints based on the data sets (upper triangles) with either the A or B group of contacts modified. (1) Reduction of the influence of restraints based on the A group of contacts on the simulation with respect to the original contact data in (a) by diffusing these contacts. Intensification of the effect of B contact-based restraints by increasing the number of these contacts (2) and by increasing the scaling factor in the restraint potential corresponding to these contacts(3).