Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships

• Published in: Current topics in medicinal chemistry Vol. 18; no. 20; p. 1755
• Main Authors: Naqvi, Ahmad Abu Turab, Mohammad, Taj, Hasan, Gulam Mustafa, Hassan, Md Imtaiyaz
• Format: Journal Article
• Language: English
• Published: United Arab Emirates 01.01.2018
• Subjects: Docking; GPCR; Drug discovery; Molecular dynamics simulation; Protein-ligand interaction; Structure-function relationships
• DOI: 10.2174/1568026618666181025114157

Protein-ligand interaction is an imperative subject in structure-based drug design and protein function prediction process. Molecular docking is a computational method which predicts the binding of a ligand molecule to the particular receptor. It predicts the binding pose, strength and binding affinity of the molecules using various scoring functions. Molecular docking and molecular dynamics simulations are widely used in combination to predict the binding modes, binding affinities and stability of different protein-ligand systems. With advancements in algorithms and computational power, molecular dynamics simulation is now a fundamental tool to investigative bio-molecular assemblies at atomic level. These methods in association with experimental support have been of great value in modern drug discovery and development. Nowadays, it has become an increasingly significant method in drug discovery process. In this review, we focus on protein-ligand interactions using molecular docking, virtual screening and molecular dynamics simulations. Here, we cover an overview of the available methods for molecular docking and molecular dynamics simulations, and their advancement and applications in the area of modern drug discovery. The available docking software and their advancement including application examples of different approaches for drug discovery are also discussed. We have also introduced the physicochemical foundations of molecular docking and simulations, mainly from the perception of bio-molecular interactions.