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Author Topic: modelling ssDNA or ssRNA  (Read 14809 times)

Offline laurap

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modelling ssDNA or ssRNA
« on: November 17, 2011, 02:43:45 am »
Dear Xiang-Jun,

I would like to model an extended conformation of an ssDNA (GT(x15) sequence) and ssRNA (GU(x12) sequence). I mean, is it possible to model single strands without helical configurations (not like the half of a duplex) using 3DNA server/package?

Thanks and regards,

Laura

Offline xiangjun

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Re: modelling ssDNA or ssRNA
« Reply #1 on: November 17, 2011, 07:38:23 am »
Hi Laura,

Thanks for your interest in 3DNA and for posting on the forum.

I understand what you mean, but I do not think 3DNA (or other tools I know of) can provide you with a straight answer. It all depends -- what specifically is your definition of "an extended conformation", i.e., "single strands without helical configurations"? If you have a starting model, mutate_bases and analyze/rebuild/frame_mol in 3DNA may help.

As always, I am willing to extend 3DNA in ways that make sense to me and are useful to the community. Currently, 3-dimensional nucleic acid structure modeling is one aspect I am interested in.

Xiang-Jun
« Last Edit: March 05, 2012, 07:04:30 pm by xiangjun »

 

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.