A method of identifying a drug candidate to a target protein for inhibiting shikimate pathway comprising (a) performing a molecular program for computing a molecule conformation and orientation relative to an active site of the target protein and selecting top-rank molecules, (b) generating protein-molecule interacting profiles and identifying conserved interactions and pharmacophore spots, (c) developing homologous pharmacophore models for identifying pharmacophore hot spots, (d) rescoring molecules selected from step (a) by their homologous pharmacophore scores, (e) selecting potential molecules having the highest homologous pharmacophore scores, and (f) acquiring corresponding real compounds of the potential molecules selected from step (c) and identifying their inhibitory activity on the target protein by bioassay.