Stacking parameters (again)

[spoblete]

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.

[xiangjun]

Dear Simón Poblete,

Thanks for coming back. My response in the initial thread on "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