LAUSR

In silico rational drug design is one of the major pylons in the drug discovery process. Drugs usually act on specific targets such as proteins, DNA, and lipid bilayers. Thus, molecular docking is an essential part of the rational drug design process. Molecular docking uses specific algorithms and scoring functions to reveal the strength of the interaction of the ligand to its target. AutoDock is a molecular docking suite that offers a variety of algorithms to tackle specific problems. These algorithms include Monte Carlo Simulated Annealing (SA), a Genetic Algorithm (GA), and a hybrid local search GA, also known as the Lamarckian Genetic Algorithm (LGA). This chapter aims to acquaint the reader with the docking process using AutoDockTools (GUI of AutoDock). Furthermore, herein is described the docking process of calf thymus DNA with three metal complexes, as a potential metallo-therapeutics as also the docking process of the plant flavonoid quercetin to the antiapoptotic protein BcL-xL.