Molecular docking and molecular dynamics simulation

Computational drug discovery methods provide valuable insights into the understanding of protein–ligand interaction systems in a virtual manner. Molecular docking and thermodynamic-based molecular dynamics (MD) simulation are important toolboxes for in silico drug discovery. Molecular docking is an approach, which employs the binding modes of small molecules or macromolecules in contact with protein receptors at the atomic level. MD simulation techniques provide a significant complementary association with that of docking. These approaches are favorable in assessing the structural features of a protein–ligand, protein–protein, protein–nucleic acid, and protein–peptide complex. This chapter discusses a broad plethora of possibilities arising in drug discovery from molecular docking to MD simulation with recent developments in these techniques and elaborates on the challenges and achievements of the focused approaches.