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Questions and answers => General discussions (Q&As) => Topic started by: jzhang71 on December 17, 2020, 09:42:59 pm

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Title: How 3DNA calculate base overlapping?
Post by: jzhang71 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!

Title: Re: How 3DNA calculate base overlapping?
Post by: xiangjun on December 27, 2020, 02:28:29 pm

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

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