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Messages - chenjief

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RNA structures (DSSR) / 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,

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.