RNA energy tables

rmw rwadkins at cbmse.nrl.navy.mil
Tue Jul 11 20:04:36 EST 1995


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




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