Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. Molecular docking generates different possible adduct structures that are ranked and grouped together using scoring function in the software. There are many databases available, which offer information on small ligand molecules such as CSD (Cambridge Structural Database), ACD (Available Chemical Directory), MDDR (MDL Drug Data Report) and NCI (National Cancer Institute Database). While performing docking, different interacted conformers are generated and compared with each other.
Approaches of Molecular Docking
For performing molecular docking, primarily two types of approaches are used.
Simulation approach
The ligand and target is being separated by physical distance and then ligand is allowed to bind into groove of target after “definite times of moves” in its conformational space. The moves involve variations to the structure of ligand either internally (torsional angle rotations) or externally (rotations and translations). The ligand in every move in the conformational limit releases energy, as “Total Energy”.
Shape complementarity approach
This approach employs ligand and target as surface structural feature that provides their molecular interaction. The complementarity between two surfaces based on shape matching illustration helps in searching the complementary groove for ligand on target surface.
Docking is most commonly used in the field of drug design, most drugs are small organic molecules, and docking may be applied to:
Hit identification: docking combined with a scoring function can be used to quickly screen large databases of potential drugs in silico to identify molecules that are likely to bind to protein target of interest
Lead optimization: docking can be used to predict in where and in which relative orientation a ligand binds to a molecule
Bioremediation: Protein ligand docking can also be used to predict pollutants that can be degraded by enzymes
Tools
Click Docking
AutoDock
Modeller
AutoDock Vina
DOCK
GOLD
Glide
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