Molecular modeling (MM) is one of the fastest growing fields in science. It may vary from building and visualizing simple molecules in three dimensions (3D) to performing complex computer simulations on large proteins and nanostructures. MM is a collection of computer-based techniques for driving, representing and manipulating the structures and reactions of molecules, and those properties that are dependent on these 3D structures. The techniques in MM cover several issues among them computational chemistry, drug design, computational biology, nanostructures, and material science.