Ligand docking methods

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

An even more complex approach is to evaluate the interaction between the chemical substance and the biological receptor at the basis of the biochemical process. Docking methods are used, which need a tridimensional description of both the receptors and the chemical ligand. Docking methods and CoMFA are very useful for certain endpoints of interest for regulation, such as endocrine disruptor studies. However, these methods do not represent the typical QSAR models for regulatory purposes [10]. 

Docking Models Based on Homology Modeling and Ligand Docking Methods. .. 287... 

Koska, J., Spassov, V.Z., Maynard, A.J., Yan, L., Austin, N., Flook, P.K., and Venkatachalam, C.M. (2008) Fully automated molecular mechanics based induced fit protein-ligand docking method. Journal of Chemical Information and Modeling, 48 (10), 1965-1973. 

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. 

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

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... 

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. 

Brooijmans, N., and Kuntz, 1. Principles and methods of docking and ligand design. Methods Biochem. Anal. 2003, 44, 443-476. 

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