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Topics - chubetty

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Hi Xiang-Jun,
I ran DSSR and find_pair|cehs on the same pdb file and noticed that the base-pair parameter values for shear, stretch, stagger, buckle, propeller, and opening are all very different. Even in the same DSSR output file, the bp-pars (Line 6) have differences with the Simple-bpParams (Line 5). I have read through El Hassan and Callandine (1995), J. Mol. Biol, 251,648-664, but am still unclear about the mathematical basis for the parameters. Could you give a simple explanation as to why the values are different within the DSSR output file and between the DSSR and find_pair|cehs output files? How would you decide which values to use for structural analysis?
Thank you very much!

RNA structures (DSSR) / Quantifying base stacking interactions
« on: August 17, 2017, 03:07:53 pm »
Hi Xiang-Jun,

I am analyzing the base stacking interactions, which I generated using the --non-pair option, in my DNA model. If I were to quantify the amount of base stacking interactions by using the numbers in and out of parentheses, would the units just be Angstroms^2? And would you define these numbers as area of overlap of the bases?

Thank you!

Betty Chu

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.