RNA2D3D accepts the primary RNA sequence information and a secondary structure representation for the sequence, which may include pseudoknots (Martinez et al. 2008). It rapidly generates a first-pass, three-dimensional model from the secondary structure. Further refinements of the models are usually necessary, but in many cases the first pass model will give significant insights as to how to proceed. Because of its speed and because of the flexibility of its structure editing tools, RNA2D3D can be used to quickly explore alternative 3D conformations in an interactive fashion (Note that it is not a de novo 3D structure prediction program.).
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J Biomol Struct Dyn. 2008 Jun;25(6):669-83.
RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.
Martinez HM, Maizel JV Jr, Shapiro BA.