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Author Topic: Definition of Helix Form  (Read 697 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/

Offline lvelve0901

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Re: Definition of Helix Form
« Reply #2 on: September 15, 2017, 05:03:35 pm »
Hi Xiangjun,

Could you please tell me when you will report the detail of helix form definition in dssr? My advisor asked me some questions in terms of how dssr identify helix form so I would like to know more details of this.

This is not urgent so please take your time.

Thank you so much.

Best,
Honglue

Offline xiangjun

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Re: Definition of Helix Form
« Reply #3 on: September 15, 2017, 11:27:50 pm »
Hi Honglue,

Thanks for your continued interest in DSSR's classifications of A-, B- and Z-helical forms. There are actually many such details in DSSR which I take as 'experimental' and are not published in the 2015 NAR paper or documented in the user manual.  Some of them will certainly end up in new publications, but no timelines.

As for DSSR reported helical forms, do they make sense? Or did you notice anything peculiar? I'd welcome your feedback.

Xiang-Jun

PS. I attended your advisor seminar (very informative) early this month at Rutgers. I saw your name in his acknowledgment list...
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.