Russian Journal of Bioorganic Chemistry

, Volume 35, Issue 6, pp 670–684 | Cite as

Prediction of the spatial structure of proteins: Emphasis on membrane targets

Review Article

Abstract

Knowledge of the spatial structure of proteins is a prerequisite for both awareness of their functional mechanisms and the framework for rational drug discovery and design. Meanwhile, direct structural determination is often hampered or impractical due to the complexity, expensiveness, and limited capabilities of experimental techniques. These issues are especially pronounced for integral membrane proteins. On numerous occasions, the theoretical prediction of protein structures may facilitate the process by exploiting physical or empirical principles. This paper surveys modern techniques for the prediction of the spatial structure of proteins using computer algorithms, and the main emphasis is placed on the most “complex” targets—membrane proteins (MPs).

The first part of the review describes de novo methods based on empirical physical principles; in the second part, a comparative modeling philosophy, which accounts for the structure of related proteins, is described. Special focus is made regarding pharmacologically relevant classes of G-coupled receptors, receptor tyrosine kinases, and other MPs. Algorithms for the assessment of the models’ quality and potential fields of application of computer models are discussed.

Key words

computer modeling integral membrane proteins homology de novo folding drug design 

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Copyright information

© Pleiades Publishing, Ltd. 2009

Authors and Affiliations

  1. 1.Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia

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