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Author Topic: how to define base pair and co-stacking  (Read 464 times)

Offline chenjief

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how to define base pair and co-stacking
« on: August 01, 2019, 11:39:13 am »
Hi Dr. Lu,

I generated RNA 2D structures from PDB structures using results from DSSR.
I am working on the tertiary sturcture prediction. So i have two problem as follow,

1.How to define the base pair between base and base? and I think the parameters
are different between the different type bases.
2.How to define the co-stacking? There are several loop types, such interloop, bulge
and multiloop. How do you define the co-stacking in these cases?

Best wishes,
Chenjie

Offline xiangjun

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Re: how to define base pair and co-stacking
« Reply #1 on: August 01, 2019, 11:56:33 am »
Hi Chenjie,

Check the DSSR NAR'15 paper. For base-pair identification and characterization, the 3DNA NAR03 paper is still valid and relevant. You may check the 3DNA source code for details.

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.