Molecular modeling of epsilon RNA from hepatitis B virus

An initial model of the HBV epsilon RNA was built by the Biopolymer module of Insight II. While its three-dimensional structure was obtained through structure optimization based on molecular dynamics simulation, the two active sites were found. A comparison with the experimental result indicated that the active sites may be the binding sites of the epsilon RNA in the RT-epsilon interaction. The result will be helpful to further discussion about the mechanism of RT-epsilon interaction and the study of HBV genome replication.