Protein–ligand docking is a molecular modelling

Molecular modelling

Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...

 technique. The goal of protein-ligand docking is to predict the position and orientation of a ligand

Ligand (biochemistry)

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In a narrower sense, it is a signal triggering molecule, binding to a site on a target protein.The binding occurs by intermolecular forces, such as ionic bonds, hydrogen...

 (a small molecule) when it is bound to a protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 receptor or enzyme. Pharmaceutical research employs docking techniques for a variety of purposes, most notably in the virtual screening

Virtual screening

Virtual screening is a computational technique used in drug discovery research. By using computers, it deals with the quick search of large libraries of chemical structures in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or...

 of large databases of available chemicals in order to select likely drug candidates.

Several protein–ligand docking software applications are available, such as AutoDock

AutoDock

AutoDock is a molecular modeling simulation software. Since 2009, it has been open source and is free for non-commercial usage. It is especially effective for Protein-ligand docking.-About:...

or EADock. There are also web service (Molecular Docking Server, SwissDock) that calculate the site, geometry and energy of small molecules interacting with proteins.

Protein Flexibility

Computational capacity has increased dramatically over the last decade making possible the use of more sophisticated and computationally intensive methods in computer-assisted drug design. However, dealing with receptor flexibility in docking methodologies is still a thorny issue . The main reason behind this difficulty is the large number of degrees of freedom that have to be considered in this kind of calculations. However, neglecting it leads to poor docking results in terms of binding pose prediction in real-world settings.

External links

• Step by step installation of MGLTools 1.5.2 (AutoDockTools, Python Molecular Viewer and Visual Programming Environment) on Ubuntu Linux 8.04
• Public distribution of docking software
  • AutoDock and MGLTools on Debian