Last modified on 24 August 2012.
Literature Reference:
Xia Z., Gardner D.P., Gutell R.R., and Ren P. (2010).
CoarseGrained Model for Simulation of RNA ThreeDimensional Structures.
Journal of Physical Chemistry B, 114:1349713506.
Manuscript Figures and Tables:
Figure 1.

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Figure 2. Superposition of the final snapshot from 10 ns CG simulations (colored green) and native structure (colored blue). The backbones are represented as thick sticks, and the bases are shown as lines.

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Figure 3.

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Table 1. Properties of Nine CG Particles  HTML 
Table 2. Bond Stretching Interaction Parameters for the CG Model of RNA Fitted by the Gaussian Function and Obtained from Statistical Structures  HTML 
Table 3. Bond Angle Interaction Parametiers for the CG Model of RNA Fitted by the Gaussian Function and obtained from Statistical Structures  HTML 
Table 4. Optimized CG Parameters for Nonbonded Interaction Described by Equation 9, Including Similar and Unlike Pairs of CG Atoms  HTML 
Table 5. Optimized CG Parameters for the Dihedral Interaction Term Described by Equation 8  HTML 
Table 6. Comparison of AllAtom Average rmsd's from the Native Crystal Structures for Both the CG Model and the FullAtom Models  HTML 
Table 7. Comparison of AllAtom RMSDs between the Final Structures of 100 ns SimulatedAnnealing Simulations to Their Native Structures  HTML 