I have a 50-base, artificially created RNA sequence and I would like to obtain its 3D structure.
What software should I use for this purpose?
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I suggest either Shapiro's RNA2D3D or MC-FOLD:
RNA2D3D -> http://www-lmmb.ncifcrf.gov/~bshapiro/rna2d3d/rna2d3d.html.
MC-FOLD -> http://www.major.iric.ca/MC-Pipeline/.
These programs require the 2D structure to generate the 3D structure, but you can easily find a program for that. Actually there's one on the MC-Pipeline website so you can get from the RNA sequence to the 3D structure in one place. RNA2D3D is more interactive than MC-Fold, but as far as I know there is no webserver and you have to use the Linux program. MC-Fold can be used online. It's the basis for Parisien & Major's excellent Nature paper (The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, 2008).
