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

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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

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.