The new drug discovery is found to be a time consuming and costly process. Recently, a trend towards the use of in-silico computational chemistry and molecular modeling for computer aided drug design has gained significant momentum. This review is an investigation of the applications of different software in drug design. The modern drug discovery process is steadily becoming more information driven. Structural, physicochemical and ADME information about property profiles of reference ligands, along with structural information of their target proteins, have been extremely useful for early-stage drug discovery. A number of examples have recently been reported for the successful applications of structure based drug design to the discovery of compounds with a potential to become more useful therapeutic agents. Among the reviewed software programs are applications programmed in Grid computing, window based general PBPK/PD modeling software, PKUDDS for structure based drug design, APIS, JAVA, Perl and Python, CADD as well as software including software libraries. These all programs are useful for cheminformatics approaches to drug design and discovery including QSAR studies, energy minimization as well as docking studies in drug design. Furthermore this review explains options for using different computer modeling software programs in drug discovery and design.