Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus

Figure 3

The novel (3D space-aided) approach to homology modelling. Left: the template structures of the HCV (in green) and BVDV (in blue) are shown in ribbon representation and their 3D space corresponding to the substrate channel is filled with alpha-spheres (see methods). Middle: the sum of alpha-spheres from the templates used to restrict the modelling of the Dengue polymerase. Right: the dengue polymerase model produced by the space-aided approach. The new model is enfolded up the sphere-filled cavity space of the templates, which guarantees that the space corresponding to substrates will not be occupied by parts of the protein.