There's lots of great stuff on both small and large ribosomal subunits
(Postscript output of structures) at rdp.life.uiuc.edu
Gutell, R.R., M.W. Gray, and M.N. Schnare, 1993. A compilation of
large subunit (23S and 23S-like) ribosomal RNA structures: 1993, Nuc.
Acids Res., (21)13 3055-3074.
You might also look at the loopDloop (Macintosh) program by D. Gilbert - try
Finally, two good references to some other methods are:
Eddy, S.R., and R. Durbin, 1994. RNA sequence analysis using covariance
models, Nucleic Acids Research, (22)11 2079-2088
Gutell, R.R., and C.R. Woese, 1990. Higher order structural elements in
ribosomal RNAs: Pseudo-knots and the use of noncanonical pairs, Proc.
Natl. Acad. Sci. USA, (87) 663-667.
These ref's were all given to me by various people on the net when our
lab began searching for better folding methods - thanks to all who
responded, and my apologies if the ref's are incomplete!
- Sam Mitchell
(samuelm at selway.umt.edu)