Scaling analysis on biologically motivated structures with different primary structure constraints using RNA-SSD. Scaling analysis for the median expected run time of biologically motivated structures with no primary base constraints and with bases constrained in fifty percent of random positions and fifty percent of stems. The lines represent the polynomial that best fits the data for structures with lengths 50, 75 and 100. The experiment with primary structure constraints is computationally expensive, and for this reason, fewer structures of each length were used. Note that the run times for constrained structures longer than 100 appear below the corresponding fit line.