Fig. 5
From: Fixed-parameter tractable sampling for RNA design with multiple target structures
Targeting specific energies for pseudoknotted structures using multi-dimensional Boltzmann sampling. a Linear fits between the energies in the stacking model to the realistic pseudoknot energy model by Dirks and Pierce (D&P) for initially sampled sequences and both target structures R1 and R2 (shown in b). The good match (respective R2 values of 0.846 and 0.841) enables more efficient targeting of Turner energies based on targeting stacking model energies. b Resulting D&P energy distributions for the two target structures R1 and R2 when aiming for the respective free energies − 30 and − 20,−30 and −30,−25 and −25,−20 and −30 kcal/mol. These demonstrate the effectivity of our adaptive multi-dimensional Boltzmann sampling procedure, especially by comparing the distributions to those of uniform and Boltzmann sampled sequences, with homogeneous weights 1 and eβ, respectively