FIGURE 5.

Accuracy of multibranch loop prediction without the use of coaxial stacking nearest neighbor parameters. The probabilities of all multibranch loops found in low free energy structures were calculated with the use of coaxial stacking nearest neighbor parameters, and loops with probabilities greater than the threshold were compared to the true structure. Here, the PPV (top) and sensitivity (bottom) are plotted against threshold value. The dotted line in each plot gives the PPV or sensitivity of a minimum free energy structure prediction without coaxial stacking parameters.