Friday, August 14, 2009

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 modeThe 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.
ScoringThe process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts.
RankingThe process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of binding.