DOPE is based on an improved reference state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on a sample native structure; it thus accounts for the finite and spherical shape of the native structures. It is implemented in the popular homology modeling program MODELLER and used to assess the energy of the protein model generated through many iterations by MODELLER, which produces homology models by the satisfaction of spatial restraints. The models returning the minimum molpdfs can be chosen as best probable structures and can be further used for evaluating with the DOPE score.
DOPE stands for "Discrete Optimized Potential Energy" and is a scoring function used to evaluate protein models generated by homology modeling software like MODELLER. It considers the energy of the model based on the spatial restraints imposed by the native structure, which is represented as a sphere with radius dependent on the sample's native structure.