Protein-ligand interactions in molecular modeling and structure-based drug design

Radical new opportunities for drug discovery are due to the revolution in biology over the past four decades. Major drug targets in the form of molecular components of disease processes have been developed for use in automated assays. After screening natural compounds, chemical databanks or combinatorial libraries to identify the lead compounds, the target macromolecules are used as a starting point for structure-based approaches. To study complex biological and chemical systems, pharmaceutical research incorporates molecular modeling methods and variety of drug discovery programs. For the identification and development of novel promising compounds, the combination of computational and experimental strategies is of great value. In the field of modern drug design, molecular docking methods explore the various ligand conformations adopted within the binding sites of macromolecular targets and select the best conformation. As various docking algorithms are available, an understanding of the advantages and limitations of each method is of great importance. The characterization of protein-ligand binding sites is essential for investigating new functional roles related to major biological research areas like health, food and energy. As the laboratory techniques for drug discovery are very much time-consuming and expensive, computational methods have been developed to assist drug discovery and development, and a number of automated methods have emerged to identify the promising drug candidates.