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Author Topic: BI/BII issue  (Read 2979 times)

Offline Auffinger

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BI/BII issue
« on: August 04, 2012, 02:34:45 pm »
Hi Xiang-Jun,

BI-BII feature is nice. however, the criteria e-z is probably not sufficient to define one or the other since, the way you do it, every nucleotide is either of the BI or BII type. Furthermore, I think that BI/BII is mainly used for B-DNA.

Best,

Pascal
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Offline xiangjun

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Re: BI/BII issue
« Reply #1 on: August 04, 2012, 03:13:30 pm »
As noted in the -tor output file,

Code: [Select]
          e-z: epsilon - zeta
              BI:  e-z = [-160, +20]
              BII: e-z = [+20, +200]

The criteria are based on "Nucleic acid backbone parameters" at the Jena website. Do you have another definition?

Also, the BI/BII classification is purely backbone-based (epsilon and zeta torsion angles), not specific to "B-DNA" whose definition may require characterization of the base pair geometry.

Xiang-Jun
« Last Edit: April 12, 2013, 06:43:38 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Auffinger

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Re: BI/BII issue
« Reply #2 on: August 05, 2012, 01:13:02 pm »
OK, thanks for the link, I will look more into that and reply soon.

Pascal
pascal auffinger
ibmc-cnrs
15, rue rené descartes
67084 strasbourg cedex
france

web sites:
http://www-ibmc.u-strasbg.fr/arn/Westho ... er_pub.HTM
http://www-ibmc.u-

 

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.