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Author Topic: Definition of Helix Form  (Read 364 times)

Offline lvelve0901

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Definition of Helix Form
« on: February 07, 2017, 10:44:31 pm »
Hi, xiangjun,

How is everything going?

In DSSR helices section, there is helix-form part including 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone.

My question is:
How do you identify the the helix form? Which parameter did you use to define the 'A' 'B' 'Z' form?

Best,
Honglue

Offline xiangjun

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Re: Definition of Helix Form
« Reply #1 on: February 07, 2017, 11:51:57 pm »
Hi Honglue,

Still working on what I promised (i.e., groove widths etc in JSON) -- it is not as straightforward as I originally thought, but I am making progress...

In the DSSR output, the classification of a dinucleotide step into 'A', 'B' or 'Z' is based on new scheme. The basic idea is on comparisons to 'reference' structures, even though technically more involved. The details will be reported later.

RNA helices are predominately in A-form, and DSSR targets on RNA users to begin with. However, DSSR also works for DNA where A-, B- and Z-forms all exist. The classification summary would be useful especially when A/B-form transition happens, as in 1tc3.

Best regards,

Xiang-Jun
« Last Edit: February 08, 2017, 11:12:12 am by xiangjun »
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.