DOPE

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DOPE, or Discrete Optimized Protein Energy, is a statistical potential used to assess homology models 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. DOPE assessment can return a score not only for the entire structure being assessed but also for each individual atom, which can be used to extract information about the restraints.

[edit] References

1. M.-y. Shen and A. Sali. Statistical potential for assessment and prediction of protein structures. Protein Science 15, 2507-2524, 2006.
2. D. Eramian, M.-y. Shen, D. Devos, F. Melo, A. Sali, and M.A. Marti-Renom. A composite score for predicting errors in protein structure models. Protein Science 15, 1653-1666, 2006.
3. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
4. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
5. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.

[edit] External links

• MODELLER main site
• MODELLER manual