MOLECULAR DOCKING

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

Applications: A binding interaction between a small molecule ligand and a enzyme protein may result in activation or inhibition of the enzyme. If the protein is a receptor, ligand binding may result in agonism or antagonism. Docking is most commonly used in the field of drug design - most drugs are small organic molecules, and docking may be applied to

Hit identification - docking combined with a scoring function can be used to quickly screen large databases of potential drugs in silico to identify molecules that are likely to bind to protein target of interest.
Lead optimization - docking can 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). This information may in turn be used to design more potent and selective analogs

Docking Programs

1.AUTODOCK
2.DOCK
3.GOLD
4.ARGULAB
5.AMBER