Experimental constraints
A number of techniques are available for probing RNA structures. These techniques can determine individual components of an existing structure such as the existence of a given base pair. It is possible to add such experimental constraints to the secondary structure prediction based on free energy minimization (see figure 22.30) and it has been shown that this can dramatically increase the fidelity of the secondary structure prediction [Mathews and Turner, 2006].
Figure 22.30: Known structural features can be added as constraints to the secondary structure prediction algorithm in CLC Genomics Workbench.