MOLECULAR DOCKING

Molecular docking of a method allowing to test one molecule of molecular recognition by another, and thus provide a method for binding and binding affinity for the complex formed by two or more molecules of known structures.

In the case of the receptor protein (RB) and the ligand (L) to be the correct docking to predict how RBL complex binding at equilibrium in aqueous solution described by equation (2)

[RBL] ↔ [RB] + [L] (2)

Figure 1: Azurine-CNT complex [RBL] , receptor - Modified Carbon Nanotube [RB], ligand - Azurine [L] A measure of the stability of the resulting complex is RBL binding free energy - VGB, which is related to the affinity of binding to or otherwise association constant of the complex according to the formula:

VGB = - RT ln (Ka)

, where R - gas constant, T - temperature, and Ka - the association constant concentration equal to the ratio of concentrations of the complex RBL-free ingredients RB and L (Ka = [RBL] / [RB] [L]) .

Docking ligand to the receptor protein comprises two consecutive processes: sampling and scoring. Sampling consists of generating different conformations of ligand-receptor binding site. This is achieved by taking into account both the sampling of conformational flexibility of the ligand and the receptor protein.

Docking methods based on ligand binding and conformational sampling include: matching shapes and ligand binding site in the receptor protein, the search for systematic and stochastic algorithm. The protein conformational sampling is sometimes considered by: soft docking, molecular relaxation, taking into account the docking side chain flexibility and involving multiple conformations of the receptor. The use of evaluation functions are empirical and are based on knowledge or derived from the use of molecular mechanics force fields.

During doking, the interaction energy of the protein with the metal surface is described by three main terms: van der Waals energy described by site-site Lennard-Jones, E.LJ, interactions (which also include weak chemical binding of aromatic residues, sulfur and histidine nitrogen atoms to graphite electrode), adsorbate – metal surface,, Umds. The electrostatic term arises from surface polarization and is represented by an image-charge term.

Softwares for molecular docking

There are a lot of programs for molecular docking, both commercial and free available.
The best-known programs include: Autodock, Autodock Vina, DOCK, DockVision, GOLD, ICM, PSI-DOCK and Vegaz ZZ.