Question: Where Is The Experimental Rna Structure Data?
0
gravatar for Veewhy
8.6 years ago by
Veewhy10
Denmark
Veewhy10 wrote:

There are several algorithms which attempt to predict the secondary structure of RNA molecules such as Vienna, but, it seems, precious little experimental data. Some structures, such as tRNA, have been solved via X-Ray crystallography and NMR, but there seems to be no general repository of RNA structures, akin to the RCSB PDB repository for proteins. I have very little knowledge of NMR/X-ray crystallography, but it seems that determination of RNA structures would be simpler than protein structures due to their smaller sizes (though perhaps this is offset by their greater flexibility?). I'd wager that experimentally derived structure data would be vastly useful for RNA-targeted drug design, and evaluation of secondary-structure prediction algorithms.

What I'd like to hear opinions on is: a) Are there ongoing efforts to determine tertiary RNA structures, and if not, why not - is it a lack of interest, or is there a technical barrier? and b) Is there a central repository for RNA structures akin to RCSB PDB database, and if so, where is it located? The only thing I found was RNABase which returns an error and an ugly message saying it has been discontinued.

rna structure • 2.2k views
ADD COMMENTlink modified 4.4 years ago by lukaskoz20 • written 8.6 years ago by Veewhy10
5
gravatar for Paul Gardner
8.6 years ago by
Paul Gardner190
Christchurch, New Zealand.
Paul Gardner190 wrote:

a) Yes. There are many solved RNA structures. They're in the PDB too, or if you prefer a specialised resource try the NDB. FRABASE is another useful resource that has parsed secondary structures from the published tertiary structures - useful for the evaluating the prediction tools. Also, check out the articles on SHAPE and SHAPE-seq - large scale probing experiments of RNA secondary structures.

b) PDB and NDB.

ADD COMMENTlink written 8.6 years ago by Paul Gardner190
0
gravatar for lukaskoz
4.4 years ago by
lukaskoz20
lukaskoz20 wrote:

alternative:

ftp://genesilico.pl/lukaskoz/rnapdb/

 

1) Solving RNA structures is much, much more harder (contrary to intuition)

2) See also RNApuzzle

ADD COMMENTlink written 4.4 years ago by lukaskoz20
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