Docking:
In molecular modeling field, docking is a method which assumes the desired orientation of one molecule to a second molecule when bound to each other, to form a stable complex. Knowledge of the orientations can be used to assume the strength of association or binding affinity between the two molecules. The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a key role in signal transduction. Thus, the relative alignment of the two interacting proteins can affect the type of signal produced. Therefore, docking is used for predicting (assuming) both the strength and the type of signal produced.
Molecular docking is one of the most frequently used methods in structure-based …show more content…
One is to use a matching technique which describes the protein and the ligand as complementary surfaces. And the second is to simulate the actual docking process in which the ligand-protein pairwise interaction energies are calculated. Both approaches have meaningful but quite different advantages and some some limitations. These are:
Shape complementarity: The complementarity between the two surfaces accounts for the shape matching description which helps in finding the complementary pose of docking the target and the ligand molecules. Another one is to describe the hydrophobic features of a protein using turns in the main-chain atoms.
Simulation: This approach seems to be very complicated. In this approach, protein and ligand are separated at some distance, and the ligand finds its position into the protein’s active site after some “moves” in its conformational space. The moves incorporate the rigid body transformations such as translations and rotations, and also the internal changes to the ligand’s structure including torsion angle rotations. Each of these moves in the conformation space of the ligand utilizes a total energetic cost of the system. That’s why the system's total energy is calculated after each and every move. This is a very expensive
In molecular modeling field, docking is a method which assumes the desired orientation of one molecule to a second molecule when bound to each other, to form a stable complex. Knowledge of the orientations can be used to assume the strength of association or binding affinity between the two molecules. The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a key role in signal transduction. Thus, the relative alignment of the two interacting proteins can affect the type of signal produced. Therefore, docking is used for predicting (assuming) both the strength and the type of signal produced.
Molecular docking is one of the most frequently used methods in structure-based …show more content…
One is to use a matching technique which describes the protein and the ligand as complementary surfaces. And the second is to simulate the actual docking process in which the ligand-protein pairwise interaction energies are calculated. Both approaches have meaningful but quite different advantages and some some limitations. These are:
Shape complementarity: The complementarity between the two surfaces accounts for the shape matching description which helps in finding the complementary pose of docking the target and the ligand molecules. Another one is to describe the hydrophobic features of a protein using turns in the main-chain atoms.
Simulation: This approach seems to be very complicated. In this approach, protein and ligand are separated at some distance, and the ligand finds its position into the protein’s active site after some “moves” in its conformational space. The moves incorporate the rigid body transformations such as translations and rotations, and also the internal changes to the ligand’s structure including torsion angle rotations. Each of these moves in the conformation space of the ligand utilizes a total energetic cost of the system. That’s why the system's total energy is calculated after each and every move. This is a very expensive