3
$\begingroup$

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?

$\endgroup$
4
$\begingroup$

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).

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.