Question

What are key ingredients required for docking?What is the difference between a ligand like benzene and a ligand like n-hexane? What can you do to account for this difference when docking the two ligands separately into the same binding pocket of the protein named T4 Lysozyme? For receptors that can undergo a large conformational change like G-protein coupled receptor (GPCR), what can you do in docking to account for this flexibility?

Answer 1

Molecular docking is the study of how two or more molecular structures (e.g., drung and enzyme or protein) fit together. In a simple definition, docking is a molecular technique that is used to predict how a protein (enzyme) interacts with small molecules (ligands).

Blinding mode- the orientation of the ligand relative to the receptor as well as the confirmation of the ligand and receptor when bound to each other.

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions.

To perform a docking screen, the first requirement is a structure of the protein of interest. Usually the structure has been determined using a biophysical technique such as x-ray crystallography, NMR spectroscopy, etc. The success of a docking program depends on two components: the search algorithm and the scoring function.

The benzene and the cyclopentadienyl ligands as formally neutral and monoanionic ligands, respectively, are potential donors og 6 π-electrons but the number of electrons effectively shared with the metal depends on the coordination mode and consequently can be lower than or equal to 6. n-hexaneis also a structural isomer of hexane and is an unbranched structure.