Docking (molecular)

Docking (molecular)

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using for example scoring functions.

The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore docking is useful for predicting both the strength and type of signal produced.

Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs. Given the biological and pharmaceutical significance of molecular docking, considerable efforts have been directed towards improving the methods used to predict docking.

Read more about Docking (molecular):  Definition of Problem, Docking Approaches, Mechanics of Docking, Applications

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Docking (molecular) - Applications
... Dockingis most commonly used in the field of drug design — most drugs are small organic molecules, and dockingmay be applied to hit identification ... lead optimization – dockingcan be used to predict in where and in which relative orientation a ligand binds to a protein (also referred to as the binding mode or pose) ... Bioremediation – Protein ligand dockingcan also be used to predict pollutants that can be degraded by enzymes ...