In article <3trlk6$6t0 at dartvax.dartmouth.edu>
Bob.Gross at Dartmouth.EDU (Robert H. Gross) writes:
> Hi folks-
>> I am interested in obtaining energy tables for use in RNA folding
> (including stacking energies). Could some kind soul point me to a
> location on Internet for downloading this information.
>Not sure what you mean here. Energy tables for what? Energies
for some structures could be computed from Amber-type force
fields.
> Also, I would like to obtain a number of "folded" RNA structures. I am
> interested in the raw data, not the final display of the RNA secondary
> structure. In other words, I'd like the information of which base is
> paired to which other base instead of a graphic image. It seems like
> this information must be available, but I have not been able to access
> it at any of the standard RNA sites on WWW. Maybe I just don't know how
> to get at it.
> Bob Gross
> Dept. of Biology, Dartmouth College
>bob.gross at dartmouth.edu
By "raw data", I assume you mean the atomic coordinates. The best
source is likely the Brookhaven Protein Data Bank, which, despite its
name, has several RNA structures in it.
ftp: ftp.pdb.bnl.gov
gopher: gopher.pdb.bnl.gov
www: www.pdb.bnl.gov
Contact them at pdb at bnl.gov if you need general info on how to used
the PDB.
--Randy
