Docking

Docking is a term used in bioinformatics to describe the process of predicting the preferred orientation of one molecule to a second when bound to each other to form a stable complex. This process is commonly used in drug discovery where the goal is to find the orientation and position of a ligand in a protein to which it has a high binding affinity.

Overview

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.

Applications

Docking is frequently used in the field of drug discovery. Here the "ligand" is usually a small organic molecule that is predicted to bind to a protein of known three-dimensional structure. The "receptor" is known in this case and is typically a protein molecule, and the ligand is the molecule that is docked into this receptor.

Docking Challenges

Despite the many successes of docking methods, there are also many challenges. These include accurately representing the ligand and receptor flexibility, the large size of the conformational space, the scoring function problem, and the pose prediction problem.

See Also

• Molecular modeling
• Drug discovery
• Ligand (biochemistry)
• Protein–ligand docking

References

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