Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Fig 7
Effects on 3D modeling of optimal σ values and DOPE.
Effects brought by the use |Δdn| values and DOPE (with a wSP of 3.5) on the 3D modeling of target 1yd0_chain_A (colored in orange) using as a template 1yd6_chain_D (pale green). In the model built using the default MODELLER (colored in white, superposed to its target and template on the left image) the three helices shown in the image are positioned in the same conformation of the template. In the model built employing |Δdn| values and DOPE with a wSP of 3.5 (pale cyan, shown on the right) the helices are repositioned in a native-like conformation. Figures rendered with PyMOL [39].