Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
Fig 2
3D structure prediction for the paradigm dsDNA/ssDNA in the present model.
(A,B) The time-evolution of system energy, number of base-pairs, RMSD from native structure, and typical 3D conformations (from top to bottom, respectively) during the Monte Carlo simulated annealing simulation for (A) a dsDNA (PDB: 1qsk) and (B) an ssDNA (PDB: 1jve). The insets show the RMSDs of refined conformations calculated over all CG beads from the corresponding atoms in native structures. The 3D structures are shown with PyMol (http://www.pymol.org).