Docking (molecular)

Docking glossary
Receptor or host or lock
The "receiving" molecule, most commonly a protein or other biopolymer.
Ligand or guest or key
The complementary partner molecule which binds to the receptor. Ligands are most often small molecules but could also be another biopolymer.
Docking
Computational simulation of a candidate ligand binding to a receptor.
Binding mode
The orientation of the ligand relative to the receptor as well as the conformation of the ligand and receptor when bound to each other.
Pose
A candidate binding mode.
Scoring
The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts.
Ranking
The process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of binding.
Docking assessment (DA)
Procedure to quantify the predictive capability of a docking protocol.
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See also: Macromolecular docking

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex.[1] 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.

Schematic illustration of docking a small molecule ligand (green) to a protein target (black) producing a stable complex.
Docking of a small molecule (green) into the crystal structure of the beta-2 adrenergic G-protein coupled receptor (PDB: 3SN6​)

The associations between biologically relevant molecules such as proteins, peptides, 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.

Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site. Characterisation of the binding behaviour plays an important role in rational design of drugs as well as to elucidate fundamental biochemical processes.[2][3]

  1. ^ Lengauer T, Rarey M (Jun 1996). "Computational methods for biomolecular docking". Current Opinion in Structural Biology. 6 (3): 402–6. doi:10.1016/S0959-440X(96)80061-3. PMID 8804827.
  2. ^ Kitchen DB, Decornez H, Furr JR, Bajorath J (Nov 2004). "Docking and scoring in virtual screening for drug discovery: methods and applications". Nature Reviews. Drug Discovery. 3 (11): 935–49. doi:10.1038/nrd1549. PMID 15520816. S2CID 1069493.
  3. ^ Mostashari-Rad T, Arian R, Mehridehnavi A, Fassihi A, Ghasemi F (June 13, 2019). "Study of CXCR4 chemokine receptor inhibitors using QSPR andmolecular docking methodologies". Journal of Theoretical and Computational Chemistry. 178 (4). doi:10.1142/S0219633619500184. S2CID 164985789.