Understanding DNA Binding Properties of Anticancer Compounds: The study of DNA interacting compounds was focused on DNA binding properties of reactive metabolites of anticancer compounds, 5F-203 and 5-aminoflavone, using molecular dynamics simulations. I designed and co-supervised these projects for a master’s thesis during my Ph.D. tenure at NIPER. Based on binding free energy calculations and molecular electrostatic surface potential, the mechanism of DNA sequence recognition by anticancer compounds was demonstrated (J. Mol. Recog. 2014). In a separate study, the DNA intercalating mechanism of a set of anticancer compounds, which were synthesized by our collaborators, was explored using molecular docking and experimental studies (Bio. Med. Chem. Lett. 2012). From these studies, we reported a systematic protocol which included unrestricted molecular docking and MD simulations of anticancer compounds bound to DNA. The protocol can be useful to researchers working on DNA-ligand binding studies.