Searching The Conformational Space For Docking

Searching The Conformational Space For Docking

In molecular modelling, docking is a method which predicts the preferred orientation of one molecule to another when bound together in a stable complex. In the case of protein docking, the search space consists of all possible orientations of the protein with respect to the ligand. Flexible docking in addition considers all possible conformations of the protein paired with all possible conformations of the ligand.

With present computing resources, it is impossible to exhaustively explore these search spaces; instead, there are many strategies which attempt to sample the search space with optimal efficiency. Most docking programs in use account for a flexible ligand, and several attempt to model a flexible protein receptor. Each "snapshot" of the pair is referred to as a pose.