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Author Topic: Identification of Basepairs - Vertical Seperation  (Read 74 times)

Offline Tom Mülller

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Identification of Basepairs - Vertical Seperation
« on: May 15, 2020, 03:47:55 am »
Dear Xiang-Jun,

I am a student at the Technical University Darmstadt, Germany and I am
trying to implement your criteria for the identification of base pairs as described in your 2015 NAR paper.

The second criterion is that the vertical separation between the base
planes is <2.5A. However, as the planes of any two bases are usually not
parallel I am unsure how to calculate the vertical separation.

Could you please clarify the proper algorithm for calculating the
vertical separation between the two base planes?


Kind Regards

Tom Müller

Offline xiangjun

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Re: Identification of Basepairs - Vertical Seperation
« Reply #1 on: May 15, 2020, 10:10:12 am »
Hi Tom,

Thanks for your interest in implementing the DSSR algorithm for identifying base pairs. You are correct that the two bases in a pair are usually not parallel. Thus the mean the two z-axes is used for calculating the vertical separation (i.e., Rise).

Detailed description of the algorithm can be fond in the paper "Structure and Conformation of Helical Nucleic Acids: Analysis Program (SCHNAaP)" (https://doi.org/10.1006/jmbi.1997.1346). The exact algorithm in SCHNAaP was then adapted to 3DNA, and DSSR. The source code of SCHNAaP is available.

Best regards,

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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.