There are many tools but problem to build when loop is present in the microRNA and also when separate it from protein. so i want better tools for modeling the microRNA.
Years ago, I saw a presentation by Florian Mueller on his studies of the signal recognition particle (SRP - a ribonucleoprotein involved in translation of proteins at the rough endoplasmic reticulum). He was using 3D RNA modeling software (ERNA 3D) he developed to visualize the role of the RNA scaffold that makes up the SRP. His software appears to be available on the Web, according to this link: http://www.erna-3d.de/