Sean Eddy (sre at al.cam.ac.uk) wrote:
: By successfully, do you mean "the computer didn't crash in a swap
: storm", or "I got the right answers"? I suspect the first. My advice
: to someone wanting to fold a single molecule of 2.5 kb of RNA is
: "don't do it". (If you have multiple RNAs, and you're using RNA
: folding programs as a first-pass tool to help you look for a structure
: they all share, that's a different story.) RNA folding programs
: sometimes mis-predict 75 nt tRNA structures; I don't think I've seen
: one ever get a 400nt group I intron right; and I don't even want to
: think about a 2.5 kb molecule.
(i) Of course I "successful" means that the computer survived and
produced a structure that minimized the free energy MODEL -
That's all a thermodynamics folding algorithm can do by definition.
(ii) The reliability of the structure prediction can - at least in my
opinion - be enhanced by using the base pair probability matrix
instead of THE minimum free energy structure. It tells you where
you have well defined structural elements as opposed to weakly
defined regions which have lots of very different structures
with comparable energy. This type of structural information
is much less sensitive to errors in the thermodynamic parameters
than the minimum free energy structure itself.
(iii) In any case the prediction can't be better than the energy model,
hence you'll never see pseudo-knots, triple helices etc.
(iv) By the way: you DO get the group one intron structure right if
you force it to make the pseudo-knot where it belongs.
Predicting pseudoknots is impossible at present for two reasons:
 the computational effort explodes if structures at not
tree-like any more, and  there by no means sufficient data on the
thermodynamics of pseudoknotted structures.
I completely agree that whatever the computer throws up cannot be more
than an educated guess, but sometimes that helps already :-)
Peter F Stadler