The shikimate pathway is the biosynthetic route for aromatic amino acids in microbes and plants but not in animals. Due to the absence of this pathway in animals, it is the main target for action of herbicides and antimicrobial agents. All the enzymes of this pathway have been targeted for herbicide and drug development. The EPSP (5-enolpyruvylshikimate-3-phosphate) synthase is one of the important enzymes of the shikimate pathway which is also involved in the biosynthesis of various secondary metabolites essential for survival. DAHP (3-Deoxy-D-arabinoheptulosonate 7-phosphate synthase) is the first enzyme of this pathway, which is involved in the condensation of PEP (Phosphoenolpyruvate) and E4P (D- erythrose 4-phosphate) to produce DAHP. Chorismate synthase and shikimate kinase are other enzyme targets of the pathway. To develop new herbicides and drugs targeting this pathway, three dimentional (3D) structure of the target enzymes must be known. But still a large number of protein structures are not available due to difficulties in wet lab determination of protein structures. This review highlights the importance of computational techniques for structural modeling of enzymes of shikimate pathway and subsequent applications for developing new herbicides and drugs.