The representation of all-atom and CG model for an RNA pseudoknot, and 3D structure prediction for a paradigm pseudoknot in the present model.

<p>(a) The 3D structure of MMTV pseudoknot (PDB code: 1rnk) in all-atomistic (left) and our CG representation (right) as well as the schematic representation for one nucleotide in the present CG model (middle). (b) The secondary structure for MMTV pseudoknot consisting of two stems and three loops. The corresponding secondary structure elements in (a) and (b) are in same colors: Stem 1 (red), Stem 2 (green), Loop 1 (blue), Loop 2 (cyan), Loop 3 (magenta) and the 3' dangling nucleotide U (orange). (c, d) The time-evolution of the energy (top panel in (c)), the number of base pairs (middle panel in (c)), the RMSDs between predicted structures and the native structure in PDB (bottom panel in (c)), and the typical 3D structures (d) during the Monte Carlo simulated annealing simulation of the <i>Aquifex aeolicus</i> tmRNA pseudoknot PK1 (PDB code: 2g1w). The inset in bottom panel in (c) shows the zoomed portion of the figure in the interval of [1.6✕10⁷, 2✕10⁷]. The RMSDs are calculated over C beads from the corresponding C4’ atoms in native structure, and the structures in (d) are shown with the PyMol (<a href="http://www.pymol.org" target="_blank">http://www.pymol.org</a>).