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The process of drug discovery and development is a long, tedious and difficult one. Occasionally new drugs are discovered by accident, more frequently they are developed as part of an organized effort to discover new ways to treat specific disease. Today the emphasis is not only just finding new ways to treat human diseases, but also to improve the quality of life in general. The computer aided drug design technique has the ability to accomplish both these goal and to improve the efficiency of the process as well. A question that always remains in mind is that what features of particular small molecule are responsible for its biological activity? Many types of data and theories may be used to probe this question, but the classical answer to question involves molecular dissection called structure activity analysis. QSAR takes the analysis one step further by representing each molecule of series in terms of set of physical, chemical descriptor and examining the correlation of potency with the value of one or more of these physical properties.