Molecular docking

Molecular docking is an essential tool for structure-based drug design (SBDD) since it provides
significant accuracy for prediction of stable binding conformation of ligand and appropriate pocket of
the target, and their binding affinities (Fu et al., 2018). Basically, a molecular docking study shows
how the ligand and the target properly fit together, in both geometrical and energetic aspects.
Accurate predictions of binding conformations and affinities from molecular docking studies for target-
ligand complexes can provide true lead compounds for drug discovery and may substantially reduce
the experimental assays (Ferreira et al., 2015). The efficiency of docking studies depend on the: (1)
search algorithms for determination of different conformations and binding modes; and (2) scoring
functions for accurate prediction of free binding energies of each protein-ligand conformations.
Binding model, binding energy (ΔGbind), torsional free energy (ΔGtor), and the stability of protein-ligand
complexes are some useful results from molecular docking studies.
Reference:
Dar, A. M., & Mir, S. (2017). Molecular Docking: Approaches, Types, Applications and Basic
Challenges. Journal of Analytical & Bioanalytical Techniques, 08(02). doi:10.4172/2155-
9872.1000356 
Ferreira, L., dos Santos, R., Oliva, G., & Andricopulo, A. (2015). Molecular Docking and Structure-
Based Drug Design Strategies. Molecules, 20(7), 13384–
13421. doi:10.3390/molecules200713384 
Fu, Y., Zhao, J., & Chen, Z. (2018). Insights into the Molecular Mechanisms of Protein-Ligand
Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of
Oligopeptide Binding Protein. Computational and Mathematical Methods in Medicine, 2018, 1–
12. doi:10.1155/2018/3502514 
Prieto-Martínez, F., Arciniega, M., & Medina-Franco, J.. (2018). Molecular docking: current advances
and challenges. TIP Revista Especializada en Ciencias Químico-Biológicas. 21.
10.22201/fesz.23958723e.2018.0.143.