TAR RNA
TAR RNA is necessary for HIV virus to function. It has been suggested that the hairpin and bulge regions affect the activity of this RNA. In our study (JCIM 56:1748-1754 (2016)) we explore the dynamical nature of the hairpin and the bulge as well as its variability caused by changes in the sequence. On how to model this system please find guidance notes in our Tutorial.
Here we show a simple demonstration where the bulge residue (red) is coming closer to a residue in the hairpin (blue).