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Questions and answers => RNA structures (DSSR) => Topic started by: spoblete on August 27, 2019, 07:56:01 pm

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Title: Stacking parameters (again)
Post by: spoblete on August 27, 2019, 07:56:01 pm

Dear Dr. Lu,
long time ago, I asked about some specifications about the criteria for defining two bases as stacked. In that time, it was enough with the answer you kindly provided me. However, now I need to know more specifically about the parameters used for that. Is it possible to obtain them?

Best wishes,

Simón Poblete.

Title: Re: Stacking parameters (again)
Post by: xiangjun on August 27, 2019, 10:31:45 pm

Dear Simón Poblete,

Thanks for coming back. My response in the initial thread on "Stacking parameters (http://forum.x3dna.org/rna-structures/stacking-parameters)" still holds. The basic idea for defining two bases as stacked has been reported in the 2003 3DNA NAR paper and the 2015 DSSR paper. If you want to dig into details, check the 3DNA source code.

If you could elaborate specifically on what to you want to extract from DSSR for base-stacking interactions, I may be able to offer more concrete help.

Best regards,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University