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Author Topic: A-Form B-Form RNA/DNA  (Read 2034 times)

Offline drknnetz

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A-Form B-Form RNA/DNA
« on: August 12, 2015, 05:23:29 pm »
Does anyone know where to find the specifics as to how x3dna paramaterizes whether the RNA is in A form and the DNA is in B form? What coordinates does it use in the DNA molecule or RNA molecule?

Offline xiangjun

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Re: A-Form B-Form RNA/DNA
« Reply #1 on: August 12, 2015, 06:12:39 pm »
It is not clear to me what you mean. Basically, 3DNA uses the so-called Zp parameter to decide if a DNA duplex is in A- or B-form. RNA duplex is nearly always in A-form. Please see the 2003 3DNA Nucleic Acids Research paper, and the A-form conformational motifs in ligand-bound DNA structures paper for details.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline drknnetz

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Re: A-Form B-Form RNA/DNA
« Reply #2 on: August 12, 2015, 07:25:42 pm »
I was basically trying to determine what parameters were used when the software determines A form or B form so I could validate the results from the program to my MD simulations. I will read the paper, thanks for the reference. You are very prompt and helpful!

Offline metoo

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Re: A-Form B-Form RNA/DNA
« Reply #3 on: March 23, 2017, 07:53:55 am »
Dear All

Where exactly is the output for Zp written? I was unable to find a user manual or specific documentation.

Thank you !



Offline xiangjun

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Re: A-Form B-Form RNA/DNA
« Reply #4 on: March 23, 2017, 10:44:59 am »
Using 355d as an example,

Code: [Select]
find_pair 355d.pdb | analyze

Check the output file 355d.out, which contains a dedicated section that includes Zp values used in the 2000 JMB paper.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.