Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Fig 8
DOPE energy landscapes for target (A) 1dk8_chain_A and (B) 1lam_chain_A modeled using different strategies. 100 decoys were built for each strategy and their GDT-HA scores are plotted here against their DOPE energies. The strategies with the “MOD-ST” prefix adopted MODELLER-generated HDDRs and a single template (blue-shaded dots), those with the “OPT-ST” prefix adopted optimal HDDRs and a single template (orange-shaded dots) and those with the “OPT-MT” prefix adopted optimal HDDRs and multiple templates (red-shaded dots). The “SP-X.X” suffix indicates the use of DOPE with a wSP of X.X. The green dots correspond to the DOPE-minimized native target structure.