How 3DNA calculate base overlapping?

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jzhang71:
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!

xiangjun:
Please read the 2003 3DNA paper and the 2015 DSSR paper.

Xiang-Jun

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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.

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