Difference between revisions of "Part:BBa K2217021"

Revision as of 16:57, 26 October 2017

miRNA-1825 binding site on hsa-circ-0000064

We have used SimRNA [1] Tool for simulating circular structure of miRNA-1825 To model interaction binding site on hsa-circ-0000064 as SimRNA generates a circular starting conformation with the 5’ and 3’ ends close to each other as a starting structure for simulation. After specifying Secondary structure restraints using multiline dots-and-brackets format, The dots-and-brackets input is parsed and internally converted into the dedicated list of restraints. W used a default of 500 steps and 1% of the lowest energy frames taken to clustering.

References

[1] Boniecki MJ, Lach G, Dawson WK, et al. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Research. 2016;44(7):e63. doi:10.1093/nar/gkv1479.

Sequence and Features