| Docking glossary
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- 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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In the fields of computational chemistry and molecular modelling, scoring functions are mathematical functions used to approximately predict the binding affinity between two molecules after they have been docked. Most commonly one of the molecules is a small organic compound such as a drug and the second is the drug's biological target such as a protein receptor.[1] Scoring functions have also been developed to predict the strength of intermolecular interactions between two proteins[2] or between protein and DNA.[3]