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Docking glossary

• Receptor or host – The "receiving" molecule, most commonly a protein or otherbiopolymer.
• Ligand or guest – 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 theconformation 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.