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

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

Volume: 18 Issue: 20

Author(s): Ahmad Abu Turab Naqvi, Taj Mohammad, Gulam Mustafa Hasan and Md. Imtaiyaz Hassan*

Affiliation:

• Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025,India

Keywords: Protein-ligand interaction, Structure-function relationships, Docking, Molecular dynamics simulation, Drug discovery, GPCR.

Abstract: 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.

Cite this article as:

Naqvi Abu Turab Ahmad , Mohammad Taj , Hasan Mustafa Gulam and Hassan Imtaiyaz Md.*, Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships, Current Topics in Medicinal Chemistry 2018; 18 (20) . https://dx.doi.org/10.2174/1568026618666181025114157