Search cost distribution for the design of structures with primary structure constraints using RNA-SSD. Distribution of expected run time of RNA-SSD on three structures of approximately 150 bases: RND-150-n85, BIOM-150-n89 and VS ribozyme from Neurospora mitochondria. The structures were designed with two sets of primary base constraints: one where the bases are fixed at random positions and another where the bases are fixed on stems for each structure. Both sets have the same range [a, b] of constrained bases after propagation, where a and b are smallest and largest number of bases constrained if 50% of stems are fixed in a given structure. We fixed 50% plus one stem when a structure had an odd number of stems.
Aguirre-Hernández et al. BMC Bioinformatics 2007 8:34 doi:10.1186/1471-2105-8-34