Rna Data Sources???...Please Help

Question

[Suhail]

hi all,

I would like to have your comments on data source for RNA secondary structures at CRW site

http://www.rna.ccbb.utexas.edu/

I am not sure if the secondary structures presented on this site are determined experimentally (that means structures are proved to be the actual RNA structures) or if the structures are presented using some prediction methods (that means there is no proof that they are actual structures) Any comment is appreciated…

Thanks

Answer 1

[Neilfws]

The vast majority of RNA secondary structures are predicted, not determined experimentally. There are very many known RNAs and very few crystal (or other experimental) structures that contain RNA.

It is quite a confusing website, but there is a section called Methods: Structure Prediction with Comparative Sequence Analysis with more information about prediction methods.

Answer 2

[Jarretinha]

The known experimentally 2nd-ary structures are deposited in PDB (together with 3rd-ary :) ). Most came from NMR experiments.

Fortunatelly, in-silico predictors for RNA 2nd-ary structure are quite realiable and accurate. But, the on Guttel Lab the data are from comparative analysis, not from de novo predictions or experimentation. They rely on a specified known structural model. They're not all real structures, only models.

So, they're different from those on RFAM (the de facto standard). If you plan to explore completely new grounds, both information will be of some utility. By the way, RFAM has links to all known structures.

[lukaskoz]

for filtered RNA and RNA-protein structures from PDB you can go here:

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