The formation of ligand-protein complexes are critical for the correct functioning of a cell. The prediction of these interactions is important for our understanding of how the cell works and for the development of new drug molecules. Homology modeling is a method for predicting the structure of a protein based on a crystal structure template. Once a model of the protein is complete, a ligand-docking algorithm predicts the ligand-protein model interaction by searching for the best steric and energetically favorable fit. A refinement of the ligand-binding pocket improves the predicted interactions by considering the flexible nature of the ligand-binding pocket. In this chapter, we describe, from first principles, methods to identify and prepare the ligand-binding pocket in a protein model, to dock the ligand, and refine the resulting complex. © 2011 Springer Science+Business Media,LLC.
CITATION STYLE
Orry, A. J. W., & Abagyan, R. (2012). Preparation and refinement of model protein-ligand complexes. Methods in Molecular Biology, 857, 351–373. https://doi.org/10.1007/978-1-61779-588-6_16
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