Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
Fig 2
Comparisons of RMSDs between the present model and other models.
(a) The predicted 3D structures (ball-stick) with the mean RMSDs (top) and the minimum RMSDs (bottom) for four sample RNA pseudoknots (PDB codes: 2g1w, 2tpk, 1e95, and 2lc8) from their native structures (cartoon). The mean (minimum) RMSDs for three pseudoknots are 4.8 Å (3.3 Å), 4.4 Å (2.8 Å), 5.4 Å (3.5 Å) and 7.4 Å (5.1 Å), respectively, and the 3D structures are shown with the PyMol (http://www.pymol.org). (b) The predictions for the 3D structures of 17 RNA pseudoknots from the present model, from the MC-Fold/MC-Sym pipeline and from the RNAComposer. The RMSDs of predicted structures for 17 RNA pseudoknots are calculated over C beads from the corresponding C4’ atoms in native structures.