Predicting structures and stabilities for H-type pseudoknots with interhelix loops

The predicted structures for three pseudoknots. (A) For LP-PK1, Hotknots (Ren et al. 2005), ILM (Ruan et al. 2004), pknotsRE (Rivas and Eddy 1999), STAR (Gultyaev et al. 1995), and pknots-RG (Reeder and Giegerich 2004) all give poor predictions for the structure (SE = 0.5). NUPACK (Dirks and Pierce 2003) gives a relatively high SE value (SE = 0.8). Our Vfold model gives the highest accuracy with SE = 0.9. (B) For the SRV-1 pseudoknot, the ILM model fails to predict the native structure of the SRV-1 pseudoknot. (C) For the 70.8 anti-HIV aptamer, we predict a pseudoknot with a 3-nt interhelix loop. In the calculations, the temperature is 37°C for A and B and 20°C for C according to the experimental condition (Held et al. 2006a,b). Also shown in the figures are the density plot for the base-pairing probability P_ij (Equation 4). In the density plots, the horizontal and vertical axes denote the indices of the nucleotides i and j.