Structural Biochemistry/Molecular Modeling/Molecular Docking

Overview
In studying enzyme catalysis, an important factor to understand is how the substrate and enzyme interact with each other. The affinity of the substrate to the enzyme is a deciding factor to whether or not the binding in the active site occurs. There are many things that affect the affinity of the substrate to the enzyme. The surface, complementarily, flexibility and non-covalent charges are all important factors. Another influencing factor includes the orientation of the molecule. Molecular modeling is a technique used in computational chemistry, computational biology and material science to mimic the behavior of molecules to further understand its systems and how they bind to each other. A type of molecular modeling is docking. Molecular docking is a method that predicts the preferred orientation of a molecule when it binds to another molecule. It uses computers to create a 3D image of two molecules and shows how they fit together. Knowing the preferred orientation that a molecule has for another can help predict the strength of binding affinity that a substrate will have for an enzyme. A common application that molecular modeling is used for is drug design. When creating a new drug for a certain disease, molecular docking can be used to predict the binding affinity that the new drug has on the targeted protein. However, there are certain errors that can occur in relying mainly on this approach. For example, while molecular modeling can predict the preferred orientation that a drug may have for a protein, it is not able to effectively account for conformational changes that may occur. But despite this, molecular docking is still a very important technique that helps us further understand the molecular processes that occurs within the molecular level.