micha at amber.biophys.uni-duesseldorf.de () writes:
>: I am looking for the best available RNA secondary structure programs.
>: I have used GCG and pc software but find it somewhat restricted and
>: unfriendly. Any suggestions?
>My suggestion: use GCG's MFOLD (hope the X-environment makes it
>easier to use) or get the RNAFold package from :
Please dont use free energy based programs for anything serious. They
fail not because they are poorly done in any way (all respect for
authors), but because there are so many unknown factors that determine
real RNA structure. Since they are unknown, they cannot be put into a
program. Anyone who still thinks these programs can predict structures
to some degree, try this: Run the E.coli 5S rRNA sequence through, and
compare with the established secondary structure (obtained by analysis
of alignments, and verified by indirect experimental proof). If it
can go that much wrong in 120 bases, then what about larger molecules.
The situation for protein secondary structure prediction is the same,
except for the approach that David Benner et al is taking in Zurich;
among other things, they interpret the variations observed in
alignments.
In 3D the situation is also the same. Molecular dynamics doesnt work
reliably on anything but small molecules, meaning it may be good for
chemistry, but not biology. It merely suggests structures that dont
violate current knowledge, but the models often turn out to be wrong
later. For anyone who thinks the approach is still good, try apply
the best MD program to any set of solved X-Ray structures in the PDB
database, and see how they almost all start vibrating and jiggling as
they move away from the known structure during optimization.
Niels Larsen
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