In <SRE.94Jun30074507 at al.cam.ac.uk>, sre at al.cam.ac.uk (Sean Eddy) writes:
>In article <2ut37o$h9a at tierra.santafe.ede> stadler at SantaFe.edu (Peter Stadler) writes:
> >We have been successfully folding 23S RNAs on an IBM RISC 6000/550
> >with 64MByte memory and the complete genome of the phage Qbeta on
> >an maschine with 256MByte.
>>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.
>>You can look at suboptimal foldings from Michael Zuker's algorithm and
>say you succeeded because the presumed correct structure is within x%
>of the global minimum, but you can only say that because you know the
>correct structure (say, from comparative sequence analysis). If
>you're dealing with a new structure, how do you pick the correct guy
>out of the haystack of suboptimals?
>>The level of faith in RNA secondary structure prediction is sometimes
>shocking:
>>"The credibility of the resulting structures did not seem to be an
>issue. There is even an unsubstantiated rumor (worth repeating) that
>when Brosius, Noller, and their colleagues submitted the first 16S
>rRNA sequence for publication, one of the reviewers questioned why
>they had not included the molecule's secondary structure as well!"
> - Woese and Pace, in _The RNA World_, CSH Press, 1993
>>--
>- Sean Eddy
>- MRC Laboratory of Molecular Biology, Cambridge, England
>- sre at mrc-lmb.cam.ac.uk
!!! * A * M * E * N * !!!
The optimal folding(s) of any biological macromolecule is(are) the one(s)
which produce a FUNCTIONAL molecule. For most enzymes and other RNAs and
proteins, the global energy minimum structure is by definition a DEAD molecule,
since most functional molecules must cycle between several different
conformations during a round of catalysis, etc.
As any RNA biologist can tell you, a purely thermodynamics-driven folding
algorithm is guaranteed to give the WRONG answers -- that's why all CORRECT RNA
secondary structures to date (from tRNA to RNase P to Group I introns to
16S and 23S rRNA) were determined by phylogenetic comparison!
o-------------------------------------------------------------------------------o
| Peter Gegenheimer | pgegen at kuhub.cc.ukans.edu |
| Departments of Biochemistry and of Botany | voice: 913-864-3939 |
| University of Kansas | FAX : 913-864-5321 |
| 2045 Haworth Hall | "The sleep of reason produces |
| Lawrence KS 66045-2106 | monsters." Goya |
o_____________________________________________|_________________________________o
