Docking method

Finally, while pharmacophore and docking methods are still two distinct methods for VS, the distance between them appears to be growing smaller structure-based pharmacophore methods are trying to include more and more information about the binding site (Sections 3.4.2 and 3.4.3), while some docking programs have successfully incorporated pharmacophore constraints, which we discuss in the next section. 

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J M and J S Dixon 1993. A Good Ligand Is Hard to Find Automated Docking Methods. spectives in Drug Discovery and Design 1 301-319. 

Rarey M, B Kramer, T Lengauer and G Klebe 1996. A Fast Flexible Docking Method Using a Incremental Construction Algorithm. Journal of Molecular Biology 261 470-489,... 

Blaney JM, Dixon JS. A good ligand is hard to find Automated docking methods. Perspect Drug Discovery Design 1993 1 301-19. 

Taylor RD, Jewsbury PJ, Essex JW. A review of protein-small molecule docking methods. J Comput-Aided Mol Des 2002 16 151-66. 

Virtual screening uses computational docking methods to assess which of a large database of compounds will fit into the unliganded structure of the target protein. Current protocols and methods can, with up to 80% success, predict the binding position and orientation of ligands that are known to bind... 

Schneider G, Bohm H J. Virtual screening and fast automated docking methods. Drug Discov Today 2002 7 64-70. 

Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental constrnction algorithm. J Mol Biol 1996 261 470-89. 

In this section, a number of case studies (Table 5) in which different types of VS methods are combined into a hybrid workflow. Often these combine a fast, ligand or pharmacophore-based method with a later docking method. The latter is useful at the inspection stage as it allows the molecule to be reviewed within the context of the protein binding site. A poor binding pose can be an indicator of a poor fit. Furthermore, possible interactions outside the scope of the molecules used to train the ligand-based method can be identified. 

Smith, G. R. and Sternberg, M. J. (2002) Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 12,28-35. 

Rarey, M., Kramer, B., Lengauer, T., and Klebe, G.A Fast flexible docking method using an incremental constmction algorithm. /. Md. Biol. 1996, 263, 470-489. 

Automated flexible ligand docking method and its application for database search./. Comput. Chem. 1997, 78, 1812-1825. 

In this section, we will examine docking methods as tools to probe the relation between structures and functions of the CYPs. 

Docking method Template X-ray Human homology model Group/year... 

Docking Methods for Structure-Based Library Design... 

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