3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: srihari on January 23, 2010, 11:03:12 pm

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.2 (DSSR Manual) · Homepage

Title: RNA 2D structure
Post by: srihari on January 23, 2010, 11:03:12 pm

Hi,
I have generated 5000 3D structures of RNA as pdb files. I would like to get the secondary structure of all these 3D structures. Is it possible with 3DNA software? If so please let me know how to use that. I have downloaded the 3DNA software.

Thanks,
Srihari

Title: Re: RNA 2D structure
Post by: xiangjun on January 24, 2010, 07:28:38 pm

Quote from: "Srihari"

I would like to get the secondary structure of all these 3D structures. Is it possible with 3DNA software? If so please let me know how to use that.

From a 3D RNA structure in PDB format, find_pair in 3DNA can identify all the double helical regions. Maybe that would serve as a starting point?

You may also find my blog post titled "Does 3DNA work for RNA? (http://http://xiang-jun.blogspot.com/2009/07/does-3dna-work-for-rna.html)" relevant.

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University