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Hi,
Do you know how 3DNA calculate the overlapping area of bases when calculating the base stacking? By Monte Carlo method or there is an analytical solution? Is there a analytical solution of purine-purine stacking (since purine have two rings)?
Thank you very much!
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Please read the 2003 3DNA paper (https://doi.org/10.1093/nar/gkg680) and the 2015 DSSR paper (https://doi.org/10.1093/nar/gkv716).
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.