Figure 4. An example of the Vfold3D prediction: the snapshot of Vfold3D web server highlights the input sequence (32 nts for this example) and the 2D structures as defined by the base pairs.

(a) For the most probable 2D structure shown in Fig. 2, Vfold3D predicts 3D structure based on the templates from the known structures. (b) For the predicted alternative structure shown in Fig. 2, Vfold3D cannot predict the 3D structure due to the lack of the available template for the single-stranded chain between the helices.