Fitness functions for RNA structure design

An RNA design algorithm takes a target RNA structure and finds a sequence that folds into that structure. This is fundamentally important for engineering therapeutics using RNA. Computational RNA design algorithms are guided by fitness functions, but not much research has been done on the merits of these functions. We survey current RNA design approaches with a particular focus on the fitness functions used. We experimentally compare the most widely used fitness functions in RNA design algorithms on both synthetic and natural sequences. It has been almost 20 years since the last comparison was published, and we find similar results with a major new result: maximizing probability outperforms minimizing ensemble defect. The probability is the likelihood of a structure at equilibrium and the ensemble defect is the weighted average number of incorrect positions in the ensemble. We find that maximizing probability leads to better results on synthetic RNA design puzzles and agrees more often than other fitness functions with natural sequences and structures, which were designed by evolution. Also, we observe that many recently published approaches minimize structure distance to the minimum free energy prediction, which we find to be a poor fitness function.