In silico docking of raltegravir at the SIVmac251 integrase (IN) active site. Panel A: An overview of the interaction between SIVmac251 integrase (in grey), 3' processed proviral DNA (green and blue cartoons) and raltegravir (in orange). The three terminal nucleotides of the 5' DNA strand (in blue) have been removed for better clarity. Metal (Mg2+) ions are shown in magenta. Panel B: Interaction of raltegravir (shown in CPK) and the integrase amino acids susceptible to primary drug resistance mutations (cyan sticks). The protein backbone is shown by cartoons. Metal ions are presented in magenta. The catalytic triad (D64, D116 and E152) is shown in yellow. Ligand-interacting nucleotides, dC25 and dA20, are shown as thin lines. A full three-dimensional view of the complex can be obtained using the 3D coordinates provided as additional material [see Additional file 4]. Image obtained using PyMOL .