In Silico Docking: Protocols for Computational Exploration of Molecular Interactions
Neha Mathur, Siva Sai Chandragiri, Sarita Sarita, Shristhi Shandily, Krupa Mukeshbhai Santoki, Nandini Navinchandra Vadhavana, Sejal Shah, Muktesh Chandra
Abstract
In computational chemistry and drug development, in silico docking has become an indispensable tool for investigating the molecular interactions between ligands and receptors. The procedures and approaches used in in-silico docking to decipher the complex dynamics of molecular binding processes are highlighted in this chapter. The first section of the chapter explains the basic ideas behind molecular docking, focusing on the function of scoring functions and algorithms in ligand-receptor interaction prediction. The benefits and drawbacks of several docking techniques—such as flexible docking, rigid-body docking, and other docking methods—are thoroughly covered. In addition, the challenges associated with conformational flexibility, solvent effects, and ligand desolvation that arise during in-silico docking are explored. Molecular dynamics simulations and ensemble docking techniques are investigated as ways to improve the precision and dependability of docking predictions. Furthermore, using in silico docking in virtual screening, structure-based drug design, and drug discovery highlights how important it is to speed up the drug development process and reduce experimental expenses. A thorough review of in silico docking techniques is given in this chapter, along with an examination of its methodological complexities, theoretical underpinnings, and real-world uses in drug discovery and computational chemistry.