stability of rna structure

[balasubramanian]

Dear 3DNA friends,

I have a multiple models of a RNA duplex obtained after clustering of MD trjectory. The RNA is a folded structure and I am not sure if i can chose the best based on structural parameters alone as it is surely is going to give odd values. Can someone please write me how i can do it. Herewith i have attached the pdb of the RNA for your perusal. Also, is there any way/script to calculate the deformation energy for RNA.

Thanks in advance,
Balasubramanian.

[xiangjun]

Hi,

You have an interesting RNA structure. In agreement with you, I do not think that you can pick up "the best based on structural parameters alone". In addition to "give odd values" of the structural parameters, what would be your reference for your comparison? 3DNA does not fit the bill here. Maybe you could get more helpful feedbacks from mailing lists such as GROMACS, AMBER etc packages.

From a pure structural point of view, given a cluster of similar structures, one could perform all-vs-all RMSD fitting to find the "centroid" (i.e., the one with minimum overall RMSD against others) as a representative.

HTH,

Xiang-Jun