Detailed discussions of various aspects of computer aided drug discovery techniques including: molecular modeling using molecular mechanics, quantum mechanics, semi-empirical quantum mechanics, and molecular dynamics. Furthermore, different conformation search methodologies will be also considered such as systemic searches, Monte Carlo techniques, and Genetic Algorithm. Furthermore, ligand-based and receptor-based drug discovery methodologies will be covered. Ligand-based methods include various QSAR techniques (such as, classical, COMFA, COMSIA, 3D-QSAR, and COMMA) and pharmacophor-based searches. On the other hand, receptor-based methods include various de novo ligand building approaches. The discussion will cover the relevant software with some hands-on experiences.