how to define base pair and co-stacking

[chenjief]

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

[xiangjun]

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