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Author Topic: How 3DNA calculate base overlapping?  (Read 21376 times)

Offline jzhang71

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How 3DNA calculate base overlapping?
« on: December 17, 2020, 09:42:59 pm »
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!
« Last Edit: December 17, 2020, 09:51:18 pm by jzhang71 »
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Offline xiangjun

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Re: How 3DNA calculate base overlapping?
« Reply #1 on: December 27, 2020, 02:28:29 pm »
Please read the 2003 3DNA paper and the 2015 DSSR paper.

Xiang-Jun
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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