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Questions and answers > General discussions (Q&As)

RNA 2D structure

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srihari:
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

xiangjun:

--- 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.
--- End quote ---
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?" relevant.

HTH,

Xiang-Jun

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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.