Generation of RNA decoys using secondary structure information.

Len: the number of nucleotides in the molecule; Bps: the number of Watson Crick and G–U wobble base pairs in the structure; RMSD: the all-atom RMSD of the decoys with the lowest all-atom RMSD from the native structure; C4′ RMSD: the C4′ RMSD of the decoy with the lowest C4′ RMSD from the native structure. FARNA C4′ RMSD: the C4′ RMSD for the decoys with the lowest C4′ RMSD obtained by Das and Baker's FARNA method [14]. A dash indicates that no structures with good base paring (energy below 1.0 Å) were obtained. All RMSD values are measured in Ångström (Å). Lowest (best) RMSD values are highlighted with bold face.