Messages

1

General discussions (Q&As) / Re: Single Strand DNA (ssDNA) 3D structure prediction

« on: February 19, 2014, 12:53:04 am »

I followed xiangjun advice. I think it's the best way.

2

General discussions (Q&As) / Re: Single Strand DNA (ssDNA) 3D structure prediction

« on: April 06, 2012, 09:00:27 am »

Dear Xiangjun,
Thank you very much for your advices. Also thank you for the excellent paper.

Best,

3

General discussions (Q&As) / Re: Single Strand DNA (ssDNA) 3D structure prediction

« on: April 06, 2012, 04:14:25 am »

Dear Xiangjun,
With this displacement I can use Rosetta etc. But I have thought the final result that make by this method is not very good. Because as you know, the software calculate the energy between nucleic acid and try to  minimize the whole structure of energy. In your opinion it is not important that  Ts are changed to Us and calculate the whole energy of structure with Us? For example seq1 and seq2 have a same 3D structure if we suppose seq1 is an ssDNA?

seq1: ATACCAATCTTAACC
seq2: AUACCAAUCUUAACC

Thank you very much,
Mohamad

4

General discussions (Q&As) / Single Strand DNA (ssDNA) 3D structure prediction

« on: April 05, 2012, 04:26:59 am »

I have an ssDNA and want to predict its 3D structure. Can I use 3DNA?
The secondary structure of my sequence is attached. For RNA we have some software such as Rosetta to predict 3D structure but unfortunately I could not find any tools that predict tertiary structure of ssDNA? Please guide me, if 3DNA can predict this structure. If 3DNA can not do it, is there any other software to do it?   

Thanks alot