The motion cross-correlation step can help the user identifying regions that have cross-correlated motions regardless of their proximity in sequence. The view is centered in any loops that were previously selected (as summarized in the “Scaffold loop list” on the left side), and compares their motions to those of other loops in the scaffold protein. Two different metrics are shown in this view, in transparent and solid squares. The first one, represents the cross-correlations existing between two whole loop super-secondary structures (each comprised of a coiled-coil region and its flanking regular secondary structures). Positive cross-correlations indicate that the predicted motions are coincident in direction and time (with or without delay), while negative cross-correlations indicate that the motions are predicted to be in opposite directions over time. The second metric, shown in solid squares, focuses on particular regions of the loop super-secondary structure and depicts the strongest cross-correlation in between the coiled-coil region of the selected scaffold protein loop (columns) and any region (coiled-coil or flanking regular secondary structure) from any other loop of the scaffold protein (rows). This informs about loops that are particularly predicted to move in coordination with the coiled-coil part of any previously selected loop. This step helps the user to detect other parts of the protein that might be interesting to graft along previously selected loops because of potentially having compounding effects protein dynamics.