Docking software

ArgusLab:Drug design program

Materials Studio: software environment

MOE:Molecular Operating Environment

Hex:Protein-Protein Docking

PCMODEL:common molecular modeling tool

Molecular Docking

In the field of molecular modeling,docking is a method which predicts the preferred orientation of one molecule to a second when boundto each other to form a stablecomplex.Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinitybetween two molecules using for examplescoring functions.

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.