FIGURE 1.
RSIM RNA structure prediction workflow. (A) Initial RNA secondary structure constraints are defined from suboptimal secondary structures predicted using the ViennaRNA folding algorithm (Hofacker et al. 1994). (B) Multiple tertiary structures for each secondary structure are generated using guided fragment assembly. (C) Monte Carlo simulations using closed moves and a statistical potential are performed for each initial tertiary structure. (D) A graph representation is generated of the conformational space with nodes being secondary structures, colored by score, and edges being simulation paths.
