DOPE score
Encyclopedia
DOPE, or Discrete Optimized Protein Energy, is a statistical potential
used to assess homology model
s in protein structure prediction
. 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. Like the current version of the MODELLER software, DOPE is implemented in Python
and is run within the MODELLER environment. The DOPE method is generally used to assess the quality of a structure model as a whole. Alternatively, DOPE can also generate a residue-by-residue energy profile for the input model, making it possible for the user to spot the problematic region in the structure model.
Statistical potential
In protein structure prediction, a statistical potential or knowledge-based potential is an energy function derived from an analysis of known protein structures in the Protein Data Bank....
used to assess homology model
Homology modeling
Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein...
s in protein structure prediction
Protein structure prediction
Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence — that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. Structure prediction is fundamentally different from the inverse...
. 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
MODELLER
MODELLER is a computer program used in producing homology models of protein tertiary structures as well as quaternary structures . It implements a technique inspired by nuclear magnetic resonance known as satisfaction of spatial restraints, by which a set of geometrical criteria are used to create...
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. Like the current version of the MODELLER software, DOPE is implemented in Python
Python (programming language)
Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
and is run within the MODELLER environment. The DOPE method is generally used to assess the quality of a structure model as a whole. Alternatively, DOPE can also generate a residue-by-residue energy profile for the input model, making it possible for the user to spot the problematic region in the structure model.