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. Author manuscript; available in PMC: 2010 Feb 25.
Published in final edited form as: J Am Chem Soc. 2009 Feb 25;131(7):2541–2546. doi: 10.1021/ja805460e

Figure 4. DMD refinement of RNA secondary and tertiary structure.

Figure 4

(A) Three pseudoatom model in which an RNA nucleotide is represented by base (B), ribose (S) and phosphate (P) groups. Lines indicate pair-wise potentials between atoms: Bi-Bj, base pairing interactions, Bi(j)-Sj(i) interaction energies for inter-nucleotide orientation dependences. The Bi(j)-Pj(i) interaction between base and phosphate reflects rigidity of RNA helices. (B) Energy diagram for the long-range constraint potential. (C) Algorithm for DMD refinement.