3DNA Forum

Questions and answers => RNA structures (DSSR) => Topic started by: chenjief on August 01, 2019, 11:39:13 am

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Title: how to define base pair and co-stacking
Post by: chenjief 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

Title: Re: how to define base pair and co-stacking
Post by: xiangjun on August 01, 2019, 11:56:33 am

Hi Chenjie,

Check the DSSR NAR'15 paper (https://nar.oxfordjournals.org/content/43/21/e142.full). For base-pair identification and characterization, the 3DNA NAR03 paper (https://doi.org/10.1093/nar/gkg680) is still valid and relevant. You may check the 3DNA source code for details.

Best regards,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.