Figure 2.

Application (II) Backrub Ensemble Design. The input form (top) for Backrub Design contains the general settings (as in Figure 1) and in addition application-specific fields for the simulation temperature (controlling the amplitude of the structural variation in the modeled conformational ensemble), and the segment length for the Backrub simulation, as well as the number of sequences generated per structure. The output (bottom) features the backbone traces of 10 generated ensemble members in green and a representation of the dynamic regions of an Ubiquitin ensemble (from blue to white to red with increasing variability) mapped onto the ubiquitin starting structure (PDB ID code: 1UBQ). Furthermore a sequence motif of the designed core residues is shown.