Proteinligand Docking

Protein-ligand docking can be further divided into two phases. First is the sampling of protein-ligand-binding space and second is the selection of the best scoring pose(s) from the sampling process. Both phases have been approached using a variety of methods; the most popular packages are listed in Table 1.2, together with the approach employed.

Sampling of the pose space, considering all possible positions, orientations and conformations of a ligand in the protein-binding site, is crucial to the success of a method. Rigid docking programs, for example Fast Rigid Exhaustive Docking (FRED) [73], require a pre-computed conformational database containing an ensemble of conformers for each ligand; these con-formers are then rigidly docked into the protein active site. Rigid docking

Table 1.2 HIGH THROUGHPUT DOCKING PROGRAMS

Program

Strategy

Vendor

Website

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