Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus
Figure 1
(a) Stereoview of the superimposed crystal structures of the HCV [7] (ribbons in green) and BVDV [8] (ribbons in blue) RNA-dependent RNA polymerases used as templates in the modelling procedure. (b) Sequence alignment of the HCV, BVDV, and Dengue polymerases derived as described in the text. Open and red shed boxes correspond to similarities and identities, respectively. Secondary structure elements corresponding to the template structures are given on the top of the alignment and colored in green for the HCV and in blue for the BVDV RdRp crystal structures. The secondary structure prediction for the Dengue polymerase and the actual secondary structure elements of the 3D model are shown below the alignment and are colored in black and red, respectively. The RdRp conserved motifs are boxed and labelled from I to VIII. The figure was produced using the ESPrint utility [9].
