Molecular docking

Molecular docking computationally predicts how a small molecule, such as a drug candidate, can bind within a macromolecular target. It estimates binding poses and often ranks them with scoring functions.

Molecular representation: A computational encoding of a molecule's atoms, bonds, geometry, and chemical properties. Docking software uses molecular representations to describe ligands and targets.
Protein structure: The three-dimensional arrangement of atoms in a protein, including its folds and conformations. Protein docking targets are commonly represented by an experimentally determined or modeled structure.
Structure-based drug design: Drug design guided by the three-dimensional structures of biological targets and their complexes. Docking is a common computational component of structure-based design.
Isothermal titration calorimetry: An experimental method that measures heat released or absorbed during molecular binding. It measures binding thermodynamics, whereas docking estimates them computationally.
Induced fit: A binding model in which ligand association prompts conformational changes in the target. A rigid target structure can miss rearrangements triggered by ligand binding.
Conformational search: A computational exploration of the three-dimensional shapes a molecule can adopt. Docking searches ligand conformations and orientations within the binding site.
Binding site: A region of a biomolecule where another molecule can bind through chemical interactions. The search is usually restricted to a target's binding site.
Virtual screening: Computational evaluation of large compound collections to identify candidates for experimental testing. Docking can rank libraries of compounds against a target binding site.
Surface plasmon resonance: An optical technique for measuring biomolecular association and dissociation in real time. It provides experimental binding kinetics that docking does not directly predict.
Conformational selection: A binding model in which a ligand preferentially binds one of a target's pre-existing conformations. Docking against one structure may overlook alternative target states.

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