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.
Probing Protein Folding Landscape by Using Combined Force Spectroscopy and Molecular Dynamics Simulations
