An Overview of Basics, Types, Approaches, Applications, Advantages and Disadvantages of Docking

Background-Molecular docking serves as an effective method for exploring the molecular targets of nutraceuticals in the treatment of diseases. Objectives-This review focuses on understanding the basics, types, approaches, applications, advantages and disadvantages of docking. Discussion-The basics of docking involve study of the ligands and proteins. The types of docking encompass Rigid Docking, Flexible-Rigid Docking and Flexible Docking. The approaches include determination of the energy profile for the docked conformer of the ligand target and determination of the complementarity of surfaces between the ligand and the target. Applications discussed in this review are Hit identification, Lead optimization, Bioremediation, Remediation, Binding site prediction, Protein – protein/ nucleic acid interactions, Searching for lead structures for protein targets, Mechanisms of enzymatic reactions, Protein engineering, Molecular dynamics simulation and Structure elucidation. The advantages of docking like easy understanding of the mechanism of action and disadvantages of docking like everchanging dynamic nature of protein-ligand interactions making it difficult to ascertain the conformational stabilities are also explained in this article. Conclusion-Docking study can include the preferred orientation of a molecule when bound to another molecule. This information can be used to predict the strength of the association between the two molecules.