Driven by chemistry but increasingly guided by pharmacology and the clinical sciences, drug research has contributed more to the progress of medicine during the past century than any other scientific factor. Computer based drug design is an alternative to the conventional process of drug development. It involves modifying a known drug for new therapeutic indication using computer technology. It has the advantage of being cost effective and time saving. The success in this area are due to identifications of molecular targets, elucidation of 3D structures by X-ray crystallography, NMR, Data availability (for biological targets and ligand) and availability of computer aided software’s. Computational drug design can be divided into two, which are structure-based and ligand based. Ligand based makes use of the knowledge of known active and inactive molecules for chemical similarity search or Quantitative Structure-Activity Relation (QSAR). The structured based make use of the knowledge of the target protein structure and is used when the data-base of the crystalline target proteins are available. The ligand based on the other hand is used when the 3D structures of the target proteins are not available.